Running Geneid

Running geneid

Table of contents:

FASTA format
General considerations
Geneid command line options
Geneid output formats
Samples
Multi-fasta files
INDEX

FASTA format

geneid input sequences must be in FASTA format:

FASTA sequence files show this structure:

>NAME OR IDENTIFIER OF SEQUENCE ATCGTACAGCTAGCTAGCTACGTACG TCGTACGATCGATCGTAGCATCACGA GGTCAGCATCTAGCACATCACACAGC CTATCAGCTAGCATCGATCGCATCGA ...

Usually Fasta lines are 60 chars long but this is not mandatory.

General considerations

To run geneid, type

- geneid \[options\] sequence\_file where sequence\_file

is a FASTA formatted DNA sequence. Predictions are sent to the standard output. In addition, the program requires an organism specific parameters file (which can be broadly used within the phylogenetic group to which organism belongs. For instance, the human file may be used as well to predict genes in genomic sequences from vertebrates).The directory params contains several files for different organisms.

The parameters file may be speficied in three different ways:

By default, geneid will try to find a default file called param.default which must be in the same directory that the binary.
Through the enviromental var GENEID, defining the path.
Using the command line option

- geneid -P file

Geneid command line options

Selection of genomic elements to display

Selection of genomic elements to display
Flag	Action
b	Display best Start codons found on sequence
d	Display best Donor sites found on sequence
a	Display best Acceptor sites found on sequence
e	Display best Stop codons found on sequence
f	Display best First exons found on sequence
i	Display best Internal exons found on sequence
t	Display best Terminal exons found on sequence
s	Display best Single genes found on sequence
x	Display best exons (all) found on sequence
z	Display Open Reading Frames found on sequence [see -Z]
D	Display genomic sequence in predicted genes

Selection of output format
Flag	Action
-	geneid format
G	gff format
X	Extended format (gff or geneid)
M	XML output (see -m)
m	See DTD for XML output

Control prediction engine
Flag	Action
-	Predictions in both strands of sequence
W	Predictions only in forward strand of sequence
C	Predictions only in reverse strand of sequence
o	Only signal and exon prediction (gene assembling disabled)
F	Force prediction of a complete gene
O	Only gene assembling (exons provided from file)
Z	Switch ORF searching on

Re-annotation of sequences
Flag	Action
R	Include annotations (evidences) provided from file
S	Use homology to protein information (SR) provided from file

Statistical model
Flag	Action
P	Provide a new parameter file
E	Increase/decrease exon weight value

Miscellanea
Flag	Action
v	Display information during geneid running
B	Show memory requirements
h	Show list of available options

Geneid output formats

Geneid format (default)
Gff output format
Xml output format
Geneid extended output format
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Click over every available format to see a detailed description:

- Geneid Format

Gene extracted from human Chromosome 22 predictions (geneid format)

# Gene 10 (Forward). 5 exons. 787 aa. Score = 39.46 First 13358069 13358945 18.58 + 0 1 5.78 3.15 45.54 0.00 AA 1:293 gene_10 Internal 13359480 13359693 1.17 + 2 2 -2.83 0.56 18.82 0.00 AA 293:364 gene_10 Internal 13359779 13360175 4.51 + 1 0 0.30 -1.47 26.77 0.00 AA 364:496 gene_10 Internal 13368380 13368662 8.38 + 0 1 3.02 2.87 25.87 0.00 AA 497:591 gene_10 Terminal 13370754 13371343 6.83 + 2 0 6.09 0.00 21.71 0.00 AA 591:787 gene_10 >chr22|geneid_v1.2_predicted_protein_10|787_AA MALHSPQYIFGDFSPDEFNQFFVTPRSSVELPPCSGTVLCGTQAGDKLPDGQEYRRIEFG VNEVIEPSDTLLRTPSYSISSTLNPQAPEFILGCTASKTTPDGITKEASYGSIDQYPGCA LALDGSSSVEAEVLENDGVSGGLGQRERKKKKKQPPGYYSCLKDGGDDSISTEALVNGHA NSAVPNSVSAEDAEFMGDMPPSVTPRTFDSPQNSTDSVSDIVPDSPFPGALGSDTGTAGQ QEGGPGVDFGQSCFPAGAGRDTLSRTAGAQPCVGTDTTENLGVANGQILESSVNKSSLSE KDRQEDAEEYLGFILNGLHEEMLNLKKLLSPNNEKRAISNGPKNQSMKKSKKNKVKEARM NGNKSVVYQQSAKESATLQPFFTLQLDIQSDKIRTVQDALESLVARESVQGYTTKTEQEV EKSRRVTLEKLPPVLVLHLKRFVYEKTGGARSLLNILWTWKLVKNCFLQGLKIRILNATE PIGSLQWSTITATVRRRSVPWLASESPGLPQRPPRPPAAPALTTGPDVPAAAAGSACAMG LPTLEFSDYYLDSPDFRERLQCHQIELERTNKFIKELIKDGSLLTGALRTEQNSTTKSAF CQPREKSGGIPWIATQSSNGQKSLGLWTTNPESSSREDATKTDAESDCQSVASVTSPGDV SPPIDLVKKGPYGLSGLKRASASSLRSISAAEGNISYSGSIQSLTSVGSKETPKASNPDL PPKMCRRLRLDTTSSNGYQRPGSVVAAKAQLFENVGSPKPVSSGHQAKAMYSYKGEHSVS FPSHKE*

Description of columns (geneid format)

Description of columns (geneid format)
Type	Type of predicted exon: First, Internal, Terminal or Single
Positions	Start and finish positions of current exon
Score	Score (reliability) of this exon
Strand	Reading sense: forward or reverse
Frame	Left uncomplete codon length in this exon
Remainder	Right uncomplete codon length in this exon
Partial scores:	Scores (log likelihood) from: Score for both signals defining exon Protein coding potential (exon content) Homology information score (blast HSPs): provided by user
AA	Amino acids corresponding to the exon translation
Key	Gene identifier

- Gff output format

Gene extracted from a human prediction (gff format)

# Gene 2 (Reverse). 3 exons. 493 aa. Score = 25.25 cons.x8bisXs.970911 geneid_v1.2 Terminal 21839 22922 18.37 - 1 gene_2 cons.x8bisXs.970911 geneid_v1.2 Internal 23679 24029 7.99 - 1 gene_2 cons.x8bisXs.970911 geneid_v1.2 First 30732 30775 -1.11 - 0 gene_2

Description of columns (gff format)

Description of columns (gff format)
Locus	DNA Sequence locusname
Source	Prediction program which produced this file
Type	Type of predicted exon: First, Internal, Terminal or Single
Positions	Start and finish positions of current exon
Score	Score (reliability) of this exon
Strand	Reading sense: forward or reverse
Frame	Left uncomplete codon length in this exon
Key	Gene identifier

- XML output format

Gene extracted from a human prediction (XML FORMAT)

Gene extracted from a human prediction (XML format)

<?xml version="1.0" ?> <!DOCTYPE prediction SYSTEM "geneid.dtd"> <prediction locus="AF100956_AF027865" length="140000" source="geneid_v1.2" date="Thu Sep 27 12:52:58 2001" genes="10" score ="204.19"> ... <gene idGene="AF100956_AF027865.G5" strand ="fwd" exons="6" score="12.35"> <exon idExon="AF100956_AF027865.G5E1" type="First" frame="0" score="5.38"> <site idSite="AF100956_AF027865.G5E1S1" type="Start" position="65038" score="3.06" /> <site idSite="AF100956_AF027865.G5E1S2" type="Donor" position="65220" score="2.89" /> </exon> <exon idExon="AF100956_AF027865.G5E2" type="Internal" frame="0" score="-0.93"> <site idSite="AF100956_AF027865.G5E2S1" type="Acceptor" position="65872" score="2.58" /> <site idSite="AF100956_AF027865.G5E2S2" type="Donor" position="66019" score="0.44" /> </exon> <exon idExon="AF100956_AF027865.G5E3" type="Internal" frame="2" score="-0.44"> <site idSite="AF100956_AF027865.G5E3S1" type="Acceptor" position="66210" score="2.20" /> <site idSite="AF100956_AF027865.G5E3S2" type="Donor" position="66321" score="3.78" /> </exon> <exon idExon="AF100956_AF027865.G5E4" type="Internal" frame="1" score="2.57"> <site idSite="AF100956_AF027865.G5E4S1" type="Acceptor" position="66774" score="2.22" /> <site idSite="AF100956_AF027865.G5E4S2" type="Donor" position="66903" score="3.50" /> </exon> <exon idExon="AF100956_AF027865.G5E5" type="Internal" frame="0" score="4.80"> <site idSite="AF100956_AF027865.G5E5S1" type="Acceptor" position="67344" score="2.54" /> <site idSite="AF100956_AF027865.G5E5S2" type="Donor" position="67548" score="1.45" /> </exon> <exon idExon="AF100956_AF027865.G5E6" type="Terminal" frame="2" score="0.97"> <site idSite="AF100956_AF027865.G5E6S1" type="Acceptor" position="67811" score="4.31" /> <site idSite="AF100956_AF027865.G5E6S2" type="Stop" position="67899" score="0.00" /> </exon> <protein length="289"> MALLDLCGAARGQRPEWAALDAGSGGRSDPGHYSFSAQAPELALPRGMQVRTVGRSGEMQ EPTAFLRSFGGDQERNVQIEMAHGTTTLAFKFQHGVIVAVDSRATAGSYISSLRMNKVIE INPYLLGTMSGCAADCQYWERLLAKECRLYYLRNGERISVSAASKLLSNMMLQYRGMGLS MGSMICGWDKKGPGLYYVDDNGTRLSGQMFSTGSGNTYAYGVMDSGYRQDLSPEEAYDLG RRAIAYATHRDNYSGGVVNMYHMKEDGWVKVESSDVSDLLYKYGEAAL* </protein> </gene> ... </prediction>

Description of columns (gff format)

Description of columns (gff format)
XML headers	XML Version and DTD used
Prediction	Prediction as a collection of genes
Gene	Gene as a collection of exons
Exon	Gene as a couple of sites
Site	Splice site or transcription signal description
Key	Predicted protein

To see more details about XML format, click here

- Geneid extended output format

Gene extracted from a human prediction (geneid eXtended format)

# Gene 7 (Reverse). 3 exons. 476 aa. Score = 47.50 Stop 91832 91834 0.00 - ATAA Terminal 91832 92551 30.56 - 0 0 0.00 3.93 84.26 0.00 AA 237:476 gene_7 Acceptor 92551 92552 3.93 - GCGGTGGTGCGGCTGTCCCCGCAGGTG Donor 93982 93983 1.23 - AAGGTATCT Internal 93983 94263 9.83 - 2 0 1.23 2.79 32.30 0.00 AA 143:236 gene_7 Acceptor 94263 94264 2.79 - AGCTGTGAACTGTTTGTTTGCTAGGGT Donor 95208 95209 2.52 - AAGGTAACC First 95209 95635 7.11 - 0 1 2.52 -1.55 30.08 0.00 AA 1:143 gene_7 Start 95633 95635 -1.55 - TTTAGAAAGCTGAGATGATG >L1084|geneid_v1.1_predicted_protein_7|476_AA MMERIRKEMILMERGLHSPTAGKRFSSLSDSAGGAVLEALENSQHPARLSPRLPSAPLHG ALGDLPAKGKFEIDTLFNLQHPSSESTVSSEIASATESRKKPSHYSEAAAEADMSSDVEV GCSALRSPSGLGAAPLKENNAKGYTESGSVAGTTTSASGSGLGSLHGGGGGGNSGAAALG GSGSGSGADQVRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQ NRRMKDKRQRLAMSWPHPADPSFYTYMMTHAAATGSLPYPFHSHVPLHYYPHVGVTAAAA AAAASGAAAAASSPFATSIRPLDTFRALSHPYSRPELLCSFRHPGLYQAPAAAAGLNSAA SAAAAAAAAAAAASSAAAAGAPPSGSSAPCSCLSCHSSQSAAAAAAAAAAALGSRGGGGS GGGGGGGAGTAGGSDFGCSAAAPRSESGFLPYSAAVLSKTAVSPPDQRDEAPLTR*

Description of columns (geneid eXtended format)

Description of columns (geneid eXtended format)
Exon type	Type of predicted exon: First, Internal, Terminal or Single
Signal type	Type of predicted signal: Acceptor, Donor, Start or Stop codon
Positions	Start and finish positions of current exon and signals
Score	Score (reliability) of exon and signals
Strand	Reading sense: forward or reverse
Frame	Left uncomplete codon length in this exon
Remainder	Right uncomplete codon length in this exon
Partial scores (exons):	Scores (log likelihood) from: Score for both signals defining exon Protein coding potential (exon content) Homology information score (SR regions): provided by user
AA	Amino acids corresponding to the exon translation
Key	Gene identifier

Samples

Click over every example to see the corresponding output:

Prediction of acceptor splice sites
Prediction of exons
Gene prediction
Geneid samples re annotation
Geneid samples homology information
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diff - This the sequence used to generate these outputs: test.fa

- Prediction of acceptor splice sites

1. geneid (default format)

1. geneid (default) format

## date Thu Sep 27 15:21:50 2003
## source-version: geneid v 1.2 -- geneid@imim.es
## Sequence test - Length = 198285 bps
# Acceptors(+) predicted in sequence test: [0,99999]
Acceptor        1        2       0.40   +       ***********************GATC
Acceptor        6        7      -0.01   +       ******************GATCAGGCT
Acceptor       60       61       2.21   +       GCATTCTTTTCTGCTTCAATTCAGTCC
Acceptor       83       84      -0.79   +       GTCCATCCCTGACCACCCACCCAGCCA
Acceptor      140      141       4.62   +       TCCTCCACCTTCCCACTCCCACAGCTA
Acceptor      151      152      -6.25   +       CCCACTCCCACAGCTAATCAGTAGCCA
Acceptor      164      165      -1.79   +       CTAATCAGTAGCCAAACCCTTTAGATT
Acceptor      229      230       0.87   +       TCCTCTAATTATGACTTAATTCAGGCT
Acceptor      272      273       2.02   +       TAAATTATTGCTGTATTGCTACAGGAG
Acceptor      275      276      -6.95   +       ATTATTGCTGTATTGCTACAGGAGTGG
Acceptor      316      317       1.17   +       ACTGTTCATCTTGGTATGCTATAGACT
Acceptor      328      329      -4.24   +       GGTATGCTATAGACTCTTGCCCAGCAG
Acceptor      331      332      -1.50   +       ATGCTATAGACTCTTGCCCAGCAGTTT
Acceptor      353      354       0.15   +       AGTTTTGCCTCAATTCTTTAAAAGCTC
Acceptor      359      360      -4.31   +       GCCTCAATTCTTTAAAAGCTCCAGTTC
Acceptor      383      384      -0.88   +       TTCATTGTTTGAAATATCAATCAGAAC
Acceptor      424      425       0.88   +       GCTAAAATGATTGTCATTCCCCAGTTT
Acceptor      450      451      -0.95   +       TTAATATCTCTATCATCTGCTAAGTAA
Acceptor      456      457      -5.79   +       TCTCTATCATCTGCTAAGTAAAAGCAA
Acceptor      478      479      -0.15   +       AGCAAGCTCCTCCTTGTGGCGTAGCAG
Acceptor      481      482      -0.48   +       AAGCTCCTCCTTGTGGCGTAGCAGGGC
...

% bin/geneid -P param/human3iso.param -ao test.fa

2. gff format

## gff-version 2
## date Thu Sep 27 15:24:22 2003
## source-version: geneid v 1.2 -- geneid@imim.es
## Sequence test - Length = 198285 bps
# Acceptors(+) predicted in sequence test: [0,99999]
test    geneid_v1.2   Acceptor    1     2   0.40   +   .    # ***********************GATC
test    geneid_v1.2   Acceptor    6     7  -0.01   +   .    # ******************GATCAGGCT
test    geneid_v1.2   Acceptor   60    61   2.21   +   .    # GCATTCTTTTCTGCTTCAATTCAGTCC
test    geneid_v1.2   Acceptor   83    84  -0.79   +   .    # GTCCATCCCTGACCACCCACCCAGCCA
test    geneid_v1.2   Acceptor  140   141   4.62   +   .    # TCCTCCACCTTCCCACTCCCACAGCTA
test    geneid_v1.2   Acceptor  151   152  -6.25   +   .    # CCCACTCCCACAGCTAATCAGTAGCCA
test    geneid_v1.2   Acceptor  164   165  -1.79   +   .    # CTAATCAGTAGCCAAACCCTTTAGATT
test    geneid_v1.2   Acceptor  229   230   0.87   +   .    # TCCTCTAATTATGACTTAATTCAGGCT
test    geneid_v1.2   Acceptor  272   273   2.02   +   .    # TAAATTATTGCTGTATTGCTACAGGAG
test    geneid_v1.2   Acceptor  275   276  -6.95   +   .    # ATTATTGCTGTATTGCTACAGGAGTGG
test    geneid_v1.2   Acceptor  316   317   1.17   +   .    # ACTGTTCATCTTGGTATGCTATAGACT
test    geneid_v1.2   Acceptor  328   329  -4.24   +   .    # GGTATGCTATAGACTCTTGCCCAGCAG
test    geneid_v1.2   Acceptor  331   332  -1.50   +   .    # ATGCTATAGACTCTTGCCCAGCAGTTT
test    geneid_v1.2   Acceptor  353   354   0.15   +   .    # AGTTTTGCCTCAATTCTTTAAAAGCTC
test    geneid_v1.2   Acceptor  359   360  -4.31   +   .    # GCCTCAATTCTTTAAAAGCTCCAGTTC
test    geneid_v1.2   Acceptor  383   384  -0.88   +   .    # TTCATTGTTTGAAATATCAATCAGAAC
test    geneid_v1.2   Acceptor  424   425   0.88   +   .    # GCTAAAATGATTGTCATTCCCCAGTTT
test    geneid_v1.2   Acceptor  450   451  -0.95   +   .    # TTAATATCTCTATCATCTGCTAAGTAA
test    geneid_v1.2   Acceptor  456   457  -5.79   +   .    # TCTCTATCATCTGCTAAGTAAAAGCAA
test    geneid_v1.2   Acceptor  478   479  -0.15   +   .    # AGCAAGCTCCTCCTTGTGGCGTAGCAG
...

% bin/geneid -P param/human3iso.param -aoG test.fa

- Prediction of exons

geneid samples: exons

1. geneid (default) format

## date Thu Sep 27 15:31:03 2003
## source-version: geneid v 1.2 -- geneid@imim.es
## Sequence test - Length = 198285 bps
# Exons(x) predicted in sequence test: [0,99999]
Internal    2   59  -10.08  + 0 1  0.40  -6.58  -2.17  0.00  20  IRLFLSVNLLPWHSFLLQF
Internal    2   59   -8.80  + 2 2  0.40  -6.58   1.01  0.00  20  QALSLCKPAPMAFFSASI
Terminal    2   23   -5.55  + 1 0  0.40   0.00  -0.74  0.00   8  SGSFSL*
Terminal    2  115   -6.83  + 0 0  0.40   0.00  -3.92  0.00  38  IRLFLSVNLLPWHSFLLQFSPSLTTHPATHAGNLRY
L*
Terminal    2  144   -5.78  + 2 0  0.40   0.00  -1.30  0.00  48  QALSLCKPAPMAFFSASIQSIPDHPPSHPCWKSEIS
LTPPPSHSHS*
Terminal    3   25   -9.22  - 2 0  0.00  -6.33  -1.04  0.00   8  LQRERA*
Internal    7   59   -9.50  + 0 2 -0.01  -6.58  -0.11  0.00  18  ALSLCKPAPMAFFSASI
Internal    7   59  -10.55  + 1 1 -0.01  -6.58  -2.73  0.00  19  LFLSVNLLPWHSFLLQF
Terminal    7   23   -6.12  + 2 0 -0.01   0.00  -1.55  0.00   6  SFSL*
Terminal    7  115   -7.30  + 1 0 -0.01   0.00  -4.48  0.00  37  LFLSVNLLPWHSFLLQFSPSLTTHPATHAGNLRYL*
Terminal    7  144   -6.47  + 0 0 -0.01   0.00  -2.42  0.00  46  ALSLCKPAPMAFFSASIQSIPDHPPSHPCWKSEISL
TPPPSHSHS*
...

% bin/geneid -P param/human3iso.param -xo test.fa

2. gff format

## gff-version 2
## date Thu Sep 27 15:46:06 2003
## source-version: geneid v 1.2 -- geneid@imim.es
## Sequence test - Length = 198285 bps
# Exons(x) predicted in sequence test: [0,99999]
test    geneid_v1.2     Internal        2       59      -10.08  +       0
test    geneid_v1.2     Internal        2       59      -8.80   +       2
test    geneid_v1.2     Terminal        2       23      -5.55   +       1
test    geneid_v1.2     Terminal        2      115      -6.83   +       0
test    geneid_v1.2     Terminal        2      144      -5.78   +       2
test    geneid_v1.2     Terminal        3       25      -9.22   -       2
test    geneid_v1.2     Internal        7       59      -9.50   +       0
test    geneid_v1.2     Internal        7       59      -10.55  +       1
test    geneid_v1.2     Terminal        7       23      -6.12   +       2
test    geneid_v1.2     Terminal        7      115      -7.30   +       1
test    geneid_v1.2     Terminal        7      144      -6.47   +       0
test    geneid_v1.2     First          26       91      -7.08   -       0
test    geneid_v1.2     First          26       40      -6.56   -       0
test    geneid_v1.2     First          26       35      -6.35   -       0
test    geneid_v1.2     Internal       26      140      -7.80   -       1
test    geneid_v1.2     Internal       26       67      -8.90   -       0
test    geneid_v1.2     First          34       59      -9.51   +       0
test    geneid_v1.2     Single         34      144      -6.49   +       0
test    geneid_v1.2     Terminal       52      140      -9.19   -       2
test    geneid_v1.2     Terminal       52       67      -7.05   -       1    
...

% bin/geneid -GP param/human3iso.param -xo test.fa

- Gene Prediction

1. geneid (default) format

1. geneid (default) format
## date Thu Sep 27 15:54:45 2003 ## source-version: geneid v 1.2 -- geneid@imim.es ## Sequence test - Length = 198285 bps # Optimal Gene Structure. 7 genes. Score = 164.188676 # Gene 1 (Forward). 8 exons. 525 aa. Score = 25.246988 Internal 3698 3982 8.69 + 2 1 5.39 1.69 23.61 0.00 AA 1: 96 gene_1 Internal 4612 4890 5.95 + 2 1 3.01 2.36 19.33 0.00 AA 96:189 gene_1 Internal 5102 5230 1.03 + 2 1 0.20 2.06 11.69 0.00 AA 189:232 gene_1 Internal 13675 13737 0.26 + 2 1 2.23 5.66 1.33 0.00 AA 232:253 gene_1 Internal 15525 15806 4.26 + 2 1 5.61 2.81 11.79 0.00 AA 253:347 gene_1 Internal 17034 17318 3.80 + 2 1 5.76 1.67 12.10 0.00 AA 347:442 gene_1 Internal 21599 21618 0.64 + 2 0 4.61 5.66 -0.07 0.00 AA 442:448 gene_1 Terminal 23145 23375 0.61 + 0 0 5.33 0.00 7.28 0.00 AA 449:525 gene_1 test\|geneid_v1.2_predicted_protein_1\|525_AA ctPTPMWPDDLQNHTFLHTVYCQDGSPSVGLSEAYDEDQLFFFDFSQNTRVPRLPEFADW AQEQGDAPAILFDKEFCEWMIQQIGPKLDGKIPVSRGFPIAEVFTLKPLEFGKPNTLVCF VSNLFPPMLTVNWQHHSVPVEGFGPTFVSAVDGLSFQAFSYLNFTPEPSDIFSCIVTHEI DRYTAIAYWVPRNALPSDLLENVLCGVAFGLGVLGIIVGIVLIIYFRKPCSGEQSMITFL PLLLGLSLGCTGAGGFVAHVESTCLLDDAGTPKDFTYCISFNKDLLTCWDPEENKMAPCE FGVLNSLANVLSQHLNQKDTLMQRLRNGLQNCATHTQPFWGSLTNRTRPPSVQVAKTTPF NTREPVMLACYVWGFYPAEVTITWRKNGKLVMPHSSAHKTAQPNGDWTYQTLSHLALTPS YGDTYTCVVEHIGAPEPILRDWRKAVPFQADAGSKKKPGSMGAIQCHAGQHLRQTPGAEV LRVGPEGQMEDRKYIHNKKEKRQCCGVEREVQNLGFFWPWTMTSA* Gene 2 (Forward). 2 exons. 181 aa. Score = 10.263193 First 74617 74854 6.35 + 0 1 5.56 -0.98 22.75 0.00 AA 1: 80 gene_2 Terminal 74929 75233 3.91 + 2 0 -6.70 0.00 33.58 0.00 AA 80:181 gene_2 test\|geneid_v1.2_predicted_protein_2\|181_AA MAASTASQRPLKGILKDNTSTTSSMVASAEHPRGSVHEQLSKKSQKWDEMNILATYRPAD KDYGLMKIDEPSTPYHSTMAAAEGLEPKYQVQEQESSGEEDSDLSPEEREKKRQFEMRRT LHYNEGLNIKLARQLISKDLHDDDKVEEMLETAHGESMNTEESNQGSTASDQQQNKSRSS Gene 3 (Reverse). 5 exons. 203 aa. Score = 5.699872 Terminal 86249 86417 1.51 - 1 0 0.00 4.28 9.84 0.00 AA 147:203 gene_3 Internal 94859 94977 -1.65 - 0 2 2.22 2.55 2.46 0.00 AA 108:147 gene_3 Internal 96314 96443 3.31 - 1 0 5.34 4.11 7.85 0.00 AA 64:107 gene_3 Internal 97054 97185 2.74 - 1 2 0.34 2.74 15.98 0.00 AA 20: 64 gene_3 First 98244 98302 -0.20 - 0 2 3.60 1.52 5.57 0.00 AA 1: 20 gene_3 test\|geneid_v1.2_predicted_protein_3\|203_AA MAVEFDGGVVMGSDSRVSAGEAVVNRVFDKLSPLHERIYCALSGSAADAQAVADMAAYQL ELHGIELEEPPLVLAAANVVRNISYKYREDLSAHLMVAGWDQREGGQLPVWTIESSWAMN CQNSMMSEPSPDFSFLFCNKLSRAKTWAKPRSKIFFKMNVLTVTMPDLEYEQEHPFTLTE TYVVTKTYINNIFNLDKINLEN* Gene 4 (Reverse). 1 exons. 104 aa. Score = 4.755478 Single 100629 100940 4.76 - 0 0 0.00 0.42 25.01 0.00 AA 1:104 gene_4 test\|geneid_v1.2_predicted_protein_4\|104_AA MRGSAVRSSTQSARSSSTVPSHAREAPGRQRHPRGAGHLELAIGTRTPSRSRPGLGLSAP RWGLKLRVPPSPPLLAAGGGNEGGALGKSQEQADPALARSSAI* Gene 5 (Forward). 15 exons. 766 aa. Score = 46.549015 First 101952 102061 -1.42 + 0 2 1.16 0.34 6.71 0.00 AA 1: 37 gene_5 Internal 102210 102340 -0.15 + 1 1 4.04 -1.92 8.94 0.00 AA 37: 81 gene_5 Internal 103300 103505 3.34 + 2 0 4.52 4.14 7.86 0.00 AA 81:149 gene_5 Internal 103932 104129 4.76 + 0 0 3.85 -0.04 18.67 0.00 AA 150:215 gene_5 Internal 105331 105459 4.56 + 0 0 5.35 3.92 10.00 0.00 AA 216:258 gene_5 Internal 105609 105797 3.81 + 0 0 5.64 0.78 12.40 0.00 AA 259:321 gene_5 Internal 106357 106530 5.45 + 0 0 3.90 3.52 15.00 0.00 AA 322:379 gene_5 Internal 106774 106936 1.28 + 0 1 3.56 0.52 9.56 0.00 AA 380:434 gene_5 Internal 107245 107381 2.61 + 2 0 3.85 4.71 6.19 0.00 AA 434:479 gene_5 Internal 108664 108840 2.52 + 0 0 4.41 -1.36 14.21 0.00 AA 480:538 gene_5 Internal 111360 111507 1.14 + 0 1 4.01 0.44 8.68 0.00 AA 539:588 gene_5 Internal 111666 111777 4.83 + 2 2 4.40 5.44 9.82 0.00 AA 588:625 gene_5 Internal 112186 112315 4.80 + 1 0 3.55 3.50 13.92 0.00 AA 625:668 gene_5 Internal 112714 112918 6.00 + 0 1 2.72 1.65 20.97 0.00 AA 669:737 gene_5 Terminal 113402 113490 3.02 + 2 0 5.19 0.00 12.26 0.00 AA 737:766 gene_5 test\|geneid_v1.2_predicted_protein_5\|766_AA MAIPFFTGRLTDWILQDGSADTFTRNLTLMSILTIASAVLEFVGDGIYNNTMGHVHSHLQ GEVFGAVLRQETEFFQQNQTGNIMSRVTEDTSTLSDSLSENLSLFLWYLVRGLCLLGIML WGSVSLTMVTLITLPLLFLLPKKVGKWYQLLEVQVRESLAKSSQVAIEALSAMPTVRSFA NEEGEAQKFREKLQEIKTLNQKEAVAYAVNSWTTSISGMLLKVGILYIGGQLVTSGAVSS GNLVTFVLYQMQFTQAVEVLLSIYPRVQKAVGSSEKIFEYLDRTPRCPPSGLLTPLHLEG LVQFQDVSFAYPNRPDVLVLQGLTFTLRPGEVTALVGPNGSGKSTVAALLQNLYQPTGGQ LLLDGKPLPQYEHRYLHRQVAAVGQEPQVFGRSLQENIAYGLTQKPTMEEITAAAVKSGA HSFISGLPQGYDTEVDEAGSQLSGGQRQAVALARALIRKPCVLILDDATSALDANSQLQV EQLLYESPERYSRSVLLITQHLSLVEQADHILFLEGGAIREGGTHQQLMEKKGCYWAMPT EFFQSLGGDGERNVQIEMAHGTTTLAFKFQHGVIAAVDSRASAGSYISALRVNKVIEINP YLLGTMSGCAADCQYWERLLAKECRLYYLRNGERISVSAASKLLSNMMCQYRGMGLSMGS MICGWDKKGPGLYYVDEHGTRLSGNMFSTGSGNTYAYGVMDSGYRPNLSPEEAYDLGRRA IAYATHRDSYSGGVVNMYHMKEDGWVKVESTDVSDLLHQYREANQ* Gene 6 (Forward). 15 exons. 1040 aa. Score = 51.141949 First 116217 116709 1.18 + 0 1 4.46 2.44 5.09 0.00 AA 1:165 gene_6 Internal 116799 116913 4.26 + 2 2 5.85 4.63 7.42 0.00 AA 165:203 gene_6 Internal 117437 117484 0.05 + 1 2 6.31 3.70 -1.13 0.00 AA 203:219 gene_6 Internal 118677 118807 3.22 + 1 1 5.18 3.05 8.20 0.00 AA 219:263 gene_6 Internal 119091 119296 7.73 + 2 0 5.08 4.49 17.47 0.00 AA 263:331 gene_6 Internal 121626 121823 6.17 + 0 0 4.30 3.64 17.26 0.00 AA 332:397 gene_6 Internal 121989 122117 2.09 + 0 0 7.47 4.49 1.03 0.00 AA 398:440 gene_6 Internal 123644 123832 2.08 + 0 0 4.08 0.30 11.14 0.00 AA 441:503 gene_6 Internal 124010 124183 7.03 + 0 0 5.53 3.68 16.25 0.00 AA 504:561 gene_6 Internal 124361 124520 3.46 + 0 1 4.54 1.41 12.22 0.00 AA 562:615 gene_6 Internal 132128 132308 2.65 + 2 2 6.44 3.78 5.05 0.00 AA 615:675 gene_6 Internal 137494 137585 1.72 + 1 1 5.36 5.38 1.95 0.00 AA 675:706 gene_6 Internal 139123 139392 4.46 + 2 1 2.30 4.31 14.99 0.00 AA 706:796 gene_6 Internal 139835 140116 3.25 + 2 1 5.08 -0.18 13.27 0.00 AA 796:890 gene_6 Terminal 150538 150989 1.80 + 2 0 1.12 0.00 16.56 0.00 AA 890:1040 gene_6 test\|geneid_v1.2_predicted_protein_6\|1040_AA MRLPDLRPWTSLLLVDAALLWLLQGPLGTLLPQGLPGLWLEGTLRLGGLWGLLKLRGLLG FVGTLLLPLCLATPLTVSLRALVAGASRAPPARVASAPWSWLLVGYGAAGLSWSLWAVLS PPGAQEKEQDQVNNKVLMWRLLKLSRPDLPLLVAAFFFLVLAVLGETLIPHYSGRVIDIL GGDFDPHAFASAIFFMCLFSFGRHTQTNKLFDKAGTGMSSLSAGCRGGCFTYTMSRINLR IREQLFSSLLRQDLGFFQETKTGELNSRLSSDTTLMSNWLPLNANVLLRSLVKVVGLYGF MLSISPRLTLLSLLHMPFTIAAEKVYNTRHQEVLREIQDAVARAGQVVREAVGGLQTVRS FGAEEHEVCRYKEALEQCRQLYWRRDLERALYLLVRRVLHLGVQMLMLSCGLQQMQDGEL TQGSLLSFMIYQESVGSYVQTLVYIYGDMLSNVGAAEKVFSYMDRQPNLPSPGTLAPTTL QGVVKFQDVSFAYPNRPDRPVLKGLTFTLRPGEVTALVGPNGSGKSTVAALLQNLYQPTG GQVLLDEKPISQYEHCYLHSQVVSVGQEPVLFSGSVRNNIAYGLQSCEDDKVMAAAQAAH ADDFIQEMEHGIYTENPLEVHDILNFSGYFLGIMSSNERICGTKHHQHLFFQDEVMDKTI TGKLRQIVHVKQYFGMGSGWVPWVVALLVNLTRLDSSMTQGTDSPEDFVIQAKADCYFTN GTEKVQFVVRFIFNLEEYVRFDSDVGMFVALTKLGQPDAEQWNSRLDLLERSRQAVDGVC RHNYRLGAPFTVGRKVQPEVTVYPERTPLLHQHNLLHCSVTGFYPGDIKIKWFLNGQEER AGVMSTGPIRNGDWTFQTVVMLEMTPELGHVYTCLVDHSSLLSPVSVEWNAEKSSDKIQH SFMLKTLDKLVIEGTYVKIVRAIYDKPAANIILNGQNLEAFPLKTGRRQECPLSLLLFNI VLEVLARAIRQEKRIKSSQIGKEEVKVFLFADDMIIYLENPIVSAQKLLKLINNFSKVSG YKINVQKLLIFLYTNNSQA* Gene 7 (Forward). 6 exons. 314 aa. Score = 20.532181 First 159435 159556 0.89 + 0 2 1.25 6.11 4.94 0.00 AA 1: 41 gene_7 Internal 177915 177947 0.49 + 1 2 5.67 4.44 -0.19 0.00 AA 41: 52 gene_7 Internal 190046 190173 -1.22 + 1 1 2.30 0.25 6.88 0.00 AA 52: 95 gene_7 Internal 192477 192743 17.00 + 2 1 4.16 4.31 42.30 0.00 AA 95:184 gene_7 Internal 195269 195550 1.81 + 2 1 3.07 1.41 11.56 0.00 AA 184:278 gene_7 Internal 196514 196624 1.56 + 2 1 2.68 4.53 5.59 0.00 AA 278:314 gene_7 test\|geneid_v1.2_predicted_protein_7\|314_AA MRDKSSAWPHHQQSCYYNEDEGTEKRGRDGIHQTTVLIHTRDSMTFIHLVPRCTCFMVQG GFKQLKNLQEKSQQILSLEEHECNTFLHNKESLAKDFLVQFKGMCYFTNGTERVRGVARY IYNREEYGRFDSDVGEFQAVTELGRSIEDWNNYKDFLEQERAAVDKVCRHNYEAELRTTL QRQVEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETAGVVSTSLIRNG DWTFQILVMLEITPQRGDIYTCQVEHPSLQSPITVEWRAQSESAQSKMLSGIGGFVLGLI FLGLGLIIRHRGQKag
`% bin/geneid -vP param/human3iso.param test.fa`

2. gff format

## gff-version 2
## date Thu Sep 27 17:16:16 2003
## source-version: geneid v 1.2 -- geneid@imim.es
## Sequence test - Length = 198285 bps
# Optimal Gene Structure. 7 genes. Score = 164.188676
 Gene 1 (Forward). 8 exons. 525 aa. Score = 25.246988
test    geneid_v1.2     Internal          3698    3982   8.69   +       2       gene_1
test    geneid_v1.2     Internal          4612    4890   5.95   +       2       gene_1
test    geneid_v1.2     Internal          5102    5230   1.03   +       2       gene_1
test    geneid_v1.2     Internal         13675    1373   0.26   +       2       gene_1
test    geneid_v1.2     Internal         15525    1580   4.26   +       2       gene_1
test    geneid_v1.2     Internal         17034    1731   3.80   +       2       gene_1
test    geneid_v1.2     Internal         21599   21618   0.64   +       2       gene_1
test    geneid_v1.2     Terminal         23145   23375   0.61   +       0       gene_1
 Gene 2 (Forward). 2 exons. 181 aa. Score = 10.263193
test    geneid_v1.2        First         74617   74854   6.35   +       0       gene_2
test    geneid_v1.2     Terminal         74929   75233   3.91   +       2       gene_2
 Gene 3 (Reverse). 5 exons. 203 aa. Score = 5.699872
test    geneid_v1.2     Terminal         86249   86417   1.51   -       1       gene_3
test    geneid_v1.2     Internal         94859   94977  -1.65   -       0       gene_3
test    geneid_v1.2     Internal         96314   96443   3.31   -       1       gene_3
test    geneid_v1.2     Internal         97054   97185   2.74   -       1       gene_3
test    geneid_v1.2        First         98244   98302  -0.20   -       0       gene_3   
 Gene 4 (Reverse). 1 exons. 104 aa. Score = 4.755478
test    geneid_v1.2       Single        100629  100940   4.76   -       0       gene_4
 Gene 5 (Forward). 15 exons. 766 aa. Score = 46.549015
test    geneid_v1.2        First        101952  102061  -1.42   +       0       gene_5
test    geneid_v1.2     Internal        102210  102340  -0.15   +       1       gene_5
test    geneid_v1.2     Internal        103300  103505   3.34   +       2       gene_5
test    geneid_v1.2     Internal        103932  104129   4.76   +       0       gene_5
test    geneid_v1.2     Internal        105331  105459   4.56   +       0       gene_5
test    geneid_v1.2     Internal        105609  105797   3.81   +       0       gene_5
test    geneid_v1.2     Internal        106357  106530   5.45   +       0       gene_5
test    geneid_v1.2     Internal        106774  106936   1.28   +       0       gene_5
test    geneid_v1.2     Internal        107245  107381   2.61   +       2       gene_5
test    geneid_v1.2     Internal        108664  108840   2.52   +       0       gene_5
test    geneid_v1.2     Internal        111360  111507   1.14   +       0       gene_5
test    geneid_v1.2     Internal        111666  111777   4.83   +       2       gene_5
test    geneid_v1.2     Internal        112186  112315   4.80   +       1       gene_5
test    geneid_v1.2     Internal        112714  112918   6.00   +       0       gene_5
test    geneid_v1.2     Terminal        113402  113490   3.02   +       2       gene_5
 Gene 6 (Forward). 15 exons. 1040 aa. Score = 51.141949
test    geneid_v1.2        First        116217  116709   1.18   +       0       gene_6
test    geneid_v1.2     Internal        116799  116913   4.26   +       2       gene_6
test    geneid_v1.2     Internal        117437  117484   0.05   +       1       gene_6
test    geneid_v1.2     Internal        118677  118807   3.22   +       1       gene_6
test    geneid_v1.2     Internal        119091  119296   7.73   +       2       gene_6
test    geneid_v1.2     Internal        121626  121823   6.17   +       0       gene_6
test    geneid_v1.2     Internal        121989  122117   2.09   +       0       gene_6
test    geneid_v1.2     Internal        123644  123832   2.08   +       0       gene_6
test    geneid_v1.2     Internal        124010  124183   7.03   +       0       gene_6
test    geneid_v1.2     Internal        124361  124520   3.46   +       0       gene_6
test    geneid_v1.2     Internal        132128  132308   2.65   +       2       gene_6
test    geneid_v1.2     Internal        137494  137585   1.72   +       1       gene_6
test    geneid_v1.2     Internal        139123  139392   4.46   +       2       gene_6
test    geneid_v1.2     Internal        139835  140116   3.25   +       2       gene_6
test    geneid_v1.2     Terminal        150538  150989   1.80   +       2       gene_6
 Gene 7 (Forward). 6 exons. 314 aa. Score = 20.532181
test    geneid_v1.2        First        159435  159556   0.89   +       0       gene_7
test    geneid_v1.2     Internal        177915  177947   0.49   +       1       gene_7
test    geneid_v1.2     Internal        190046  190173  -1.22   +       1       gene_7
test    geneid_v1.2     Internal        192477  192743  17.00   +       2       gene_7
test    geneid_v1.2     Internal        195269  195550   1.81   +       2       gene_7
test    geneid_v1.2     Internal        196514  196624   1.56   +       2       gene_7

% bin/geneid -vGP param/human3iso.param test.fa

3. eXtended formar (default)

3. eXtended format (default)
## date Thu Sep 27 17:27:29 2003 ## source-version: geneid v 1.2 -- geneid@imim.es ## Sequence test - Length = 198285 bps # Optimal Gene Structure. 7 genes. Score = 164.188676 # Gene 1 (Forward). 8 exons. 525 aa. Score = 25.246988 Acceptor 3697 3698 5.39 + AACCTCACCCTGTGTCCTTTGCAGCTC Internal 3698 3982 8.69 + 2 1 5.39 1.69 23.61 0.00 AA 1: 96 gene_1 Donor 3982 3983 1.69 + GAGGTCAGG Acceptor 4611 4612 3.01 + CCTACACTTCAATCCCCCCACCAGGGT Internal 4612 4890 5.95 + 2 1 3.01 2.36 19.33 0.00 AA 96:189 gene_1 Donor 4890 4891 2.36 + GGGGTGAGG Acceptor 5101 5102 0.20 + GGCTGAGCCACTCATTTCCTCCAGTAC Internal 5102 5230 1.03 + 2 1 0.20 2.06 11.69 0.00 AA 189:232 gene_1 Donor 5230 5231 2.06 + GTGGTATGT Acceptor 13674 13675 2.23 + ACTGAACTCCCGGCATCTTTACAGAGC Internal 13675 13737 0.26 + 2 1 2.23 5.66 1.33 0.00 AA 232:253 gene_1 Donor 13737 13738 5.66 + CAGGTAAGG Acceptor 15524 15525 5.61 + TTCTCCCTTCCCTGGCTCCTCTAGGTG Internal 15525 15806 4.26 + 2 1 5.61 2.81 11.79 0.00 AA 253:347 gene_1 Donor 15806 15807 2.81 + CACGTGAGG Acceptor 17033 17034 5.76 + AACATGTTTTTTTCTCCTATGCAGGGC Internal 17034 17318 3.80 + 2 1 5.76 1.67 12.10 0.00 AA 347:442 gene_1 Donor 17318 17319 1.67 + GGAGTAAGT Acceptor 21598 21599 4.61 + CTTTGTAGGTTTTTTGTTTTATAGGAA Internal 21599 21618 0.64 + 2 0 4.61 5.66 -0.07 0.00 AA 442:448 gene_1 Donor 21618 21619 5.66 + CAGGTAAGG Acceptor 23144 23145 5.33 + CTCCCCTCTTCCCTCTGCTCTTAGGCT Terminal 23145 23375 0.61 + 0 0 5.33 0.00 7.28 0.00 AA 449:525 gene_1 Stop 23373 23375 0.00 + ATAG test\|geneid_v1.2_predicted_protein_1\|525_AA ctPTPMWPDDLQNHTFLHTVYCQDGSPSVGLSEAYDEDQLFFFDFSQNTRVPRLPEFADW AQEQGDAPAILFDKEFCEWMIQQIGPKLDGKIPVSRGFPIAEVFTLKPLEFGKPNTLVCF VSNLFPPMLTVNWQHHSVPVEGFGPTFVSAVDGLSFQAFSYLNFTPEPSDIFSCIVTHEI DRYTAIAYWVPRNALPSDLLENVLCGVAFGLGVLGIIVGIVLIIYFRKPCSGEQSMITFL PLLLGLSLGCTGAGGFVAHVESTCLLDDAGTPKDFTYCISFNKDLLTCWDPEENKMAPCE FGVLNSLANVLSQHLNQKDTLMQRLRNGLQNCATHTQPFWGSLTNRTRPPSVQVAKTTPF NTREPVMLACYVWGFYPAEVTITWRKNGKLVMPHSSAHKTAQPNGDWTYQTLSHLALTPS YGDTYTCVVEHIGAPEPILRDWRKAVPFQADAGSKKKPGSMGAIQCHAGQHLRQTPGAEV LRVGPEGQMEDRKYIHNKKEKRQCCGVEREVQNLGFFWPWTMTSA* Gene 2 (Forward). 2 exons. 181 aa. Score = 10.263193 Start 74617 74619 5.56 + CGGAGCACCCGGCAATGGCG First 74617 74854 6.35 + 0 1 5.56 -0.98 22.75 0.00 AA 1: 80 gene_2 Donor 74854 74855 -0.98 + TGGGTGATG Acceptor 74928 74929 -6.70 + ACAGATAGCTTGCTAAGAACTTAGCTG Terminal 74929 75233 3.91 + 2 0 -6.70 0.00 33.58 0.00 AA 80:181 gene_2 Stop 75231 75233 0.00 + ATAG test\|geneid_v1.2_predicted_protein_2\|181_AA MAASTASQRPLKGILKDNTSTTSSMVASAEHPRGSVHEQLSKKSQKWDEMNILATYRPAD KDYGLMKIDEPSTPYHSTMAAAEGLEPKYQVQEQESSGEEDSDLSPEEREKKRQFEMRRT LHYNEGLNIKLARQLISKDLHDDDKVEEMLETAHGESMNTEESNQGSTASDQQQNKSRSS Gene 3 (Reverse). 5 exons. 203 aa. Score = 5.699872 Stop 86249 86251 0.00 - TTGA Terminal 86249 86417 1.51 - 1 0 0.00 4.28 9.84 0.00 AA 147:203 gene_3 Acceptor 86417 86418 4.28 - TCGTCTCTATTTGGCCTGTTTTAGGGC Donor 94858 94859 2.22 - CTGGTATGG Internal 94859 94977 -1.65 - 0 2 2.22 2.55 2.46 0.00 AA 108:147 gene_3 Acceptor 94977 94978 2.55 - TCATCTACCTGGTCACTATTACAGCTG Donor 96313 96314 5.34 - CAGGTGAGT Internal 96314 96443 3.31 - 1 0 5.34 4.11 7.85 0.00 AA 64:107 gene_3 Acceptor 96443 96444 4.11 - CTTTATTCCTAATATTTCCCTCAGGAT Donor 97053 97054 0.34 - TGGGTATGA Internal 97054 97185 2.74 - 1 2 0.34 2.74 15.98 0.00 AA 20: 64 gene_3 Acceptor 97185 97186 2.74 - TGACTGTTGACTCCCTCCTGACAGCGA Donor 98243 98244 3.60 - AGGGTGAGT First 98244 98302 -0.20 - 0 2 3.60 1.52 5.57 0.00 AA 1: 20 gene_3 Start 98300 98302 1.52 - TGCAGACCACCATCATGGCA test\|geneid_v1.2_predicted_protein_3\|203_AA MAVEFDGGVVMGSDSRVSAGEAVVNRVFDKLSPLHERIYCALSGSAADAQAVADMAAYQL ELHGIELEEPPLVLAAANVVRNISYKYREDLSAHLMVAGWDQREGGQLPVWTIESSWAMN CQNSMMSEPSPDFSFLFCNKLSRAKTWAKPRSKIFFKMNVLTVTMPDLEYEQEHPFTLTE TYVVTKTYINNIFNLDKINLEN* Gene 4 (Reverse). 1 exons. 104 aa. Score = 4.755478 Stop 100629 100631 0.00 - TTAG Single 100629 100940 4.76 - 0 0 0.00 0.42 25.01 0.00 AA 1:104 gene_4 Start 100938 100940 0.42 - CCAGCAGGGAGAATATGCGG test\|geneid_v1.2_predicted_protein_4\|104_AA MRGSAVRSSTQSARSSSTVPSHAREAPGRQRHPRGAGHLELAIGTRTPSRSRPGLGLSAP RWGLKLRVPPSPPLLAAGGGNEGGALGKSQEQADPALARSSAI* Gene 5 (Forward). 15 exons. 766 aa. Score = 46.549015 Start 101952 101954 1.16 + TTTCTCCAGGGGAGATGGCC First 101952 102061 -1.42 + 0 2 1.16 0.34 6.71 0.00 AA 1: 37 gene_5 Donor 102061 102062 0.34 + CAGGTCTGG Acceptor 102209 102210 4.04 + CCTTTTTTTCCGGGTTCTTTATAGTGC Internal 102210 102340 -0.15 + 1 1 4.04 -1.92 8.94 0.00 AA 37: 81 gene_5 Donor 102340 102341 -1.92 + CAGGTTTCT Acceptor 103299 103300 4.52 + ACTCTCTTCTCCCCAACCCTGCAGGTA Internal 103300 103505 3.34 + 2 0 4.52 4.14 7.86 0.00 AA 81:149 gene_5 Donor 103505 103506 4.14 + CAGGTATGT Acceptor 103931 103932 3.85 + CATCTCTTGTCCATGTATCCACAGTTG Internal 103932 104129 4.76 + 0 0 3.85 -0.04 18.67 0.00 AA 150:215 gene_5 Donor 104129 104130 -0.04 + AGTGTGAGC Acceptor 105330 105331 5.35 + CCTTTTTTTGTGGTCTCTTTATAGATT Internal 105331 105459 4.56 + 0 0 5.35 3.92 10.00 0.00 AA 216:258 gene_5 Donor 105459 105460 3.92 + GAGGTGAGG Acceptor 105608 105609 5.64 + TTCACTATTCTTACCTCCCTCTAGGTA Internal 105609 105797 3.81 + 0 0 5.64 0.78 12.40 0.00 AA 259:321 gene_5 Donor 105797 105798 0.78 + CAGGTACAA Acceptor 106356 106357 3.90 + ATCGTGTGCTTCTCTGGCCTCTAGGGG Internal 106357 106530 5.45 + 0 0 3.90 3.52 15.00 0.00 AA 322:379 gene_5 Donor 106530 106531 3.52 + CAGGTATGG Acceptor 106773 106774 3.56 + ACTCTTCATCATATTTCATCTCAGGTG Internal 106774 106936 1.28 + 0 1 3.56 0.52 9.56 0.00 AA 380:434 gene_5 Donor 106936 106937 0.52 + CAGGTACTC Acceptor 107244 107245 3.85 + TCATCTTGGCCCTTTGCTCTGCAGAGG Internal 107245 107381 2.61 + 2 0 3.85 4.71 6.19 0.00 AA 434:479 gene_5 Donor 107381 107382 4.71 + CAGGTGAGG Acceptor 108663 108664 4.41 + TGACGGTCCGATGTCTTTCCTCAGGTG Internal 108664 108840 2.52 + 0 0 4.41 -1.36 14.21 0.00 AA 480:538 gene_5 Donor 108840 108841 -1.36 + ATGGTGCAG Acceptor 111359 111360 4.01 + TCTCAACCTCTTTTCTCTTATCAGCCC Internal 111360 111507 1.14 + 0 1 4.01 0.44 8.68 0.00 AA 539:588 gene_5 Donor 111507 111508 0.44 + TTAGTGAGT Acceptor 111665 111666 4.40 + TCCCAAAGCTCCATCTTCTTCCAGGTG Internal 111666 111777 4.83 + 2 2 4.40 5.44 9.82 0.00 AA 588:625 gene_5 Donor 111777 111778 5.44 + CAGGTAAGC Acceptor 112185 112186 3.55 + TCACTCCACCTTGTCCTCACCCAGGCT Internal 112186 112315 4.80 + 1 0 3.55 3.50 13.92 0.00 AA 625:668 gene_5 Donor 112315 112316 3.50 + AAGGTGGGT Acceptor 112713 112714 2.72 + AGCCTGAAATCTTTCATCTTATAGGGT Internal 112714 112918 6.00 + 0 1 2.72 1.65 20.97 0.00 AA 669:737 gene_5 Donor 112918 112919 1.65 + ATAGTAAGA Acceptor 113401 113402 5.19 + TGTTCTTTTCTCATTTGTCCACAGTGT Terminal 113402 113490 3.02 + 2 0 5.19 0.00 12.26 0.00 AA 737:766 gene_5 Stop 113488 113490 0.00 + ATAA test\|geneid_v1.2_predicted_protein_5\|766_AA MAIPFFTGRLTDWILQDGSADTFTRNLTLMSILTIASAVLEFVGDGIYNNTMGHVHSHLQ GEVFGAVLRQETEFFQQNQTGNIMSRVTEDTSTLSDSLSENLSLFLWYLVRGLCLLGIML WGSVSLTMVTLITLPLLFLLPKKVGKWYQLLEVQVRESLAKSSQVAIEALSAMPTVRSFA NEEGEAQKFREKLQEIKTLNQKEAVAYAVNSWTTSISGMLLKVGILYIGGQLVTSGAVSS GNLVTFVLYQMQFTQAVEVLLSIYPRVQKAVGSSEKIFEYLDRTPRCPPSGLLTPLHLEG LVQFQDVSFAYPNRPDVLVLQGLTFTLRPGEVTALVGPNGSGKSTVAALLQNLYQPTGGQ LLLDGKPLPQYEHRYLHRQVAAVGQEPQVFGRSLQENIAYGLTQKPTMEEITAAAVKSGA HSFISGLPQGYDTEVDEAGSQLSGGQRQAVALARALIRKPCVLILDDATSALDANSQLQV EQLLYESPERYSRSVLLITQHLSLVEQADHILFLEGGAIREGGTHQQLMEKKGCYWAMPT EFFQSLGGDGERNVQIEMAHGTTTLAFKFQHGVIAAVDSRASAGSYISALRVNKVIEINP YLLGTMSGCAADCQYWERLLAKECRLYYLRNGERISVSAASKLLSNMMCQYRGMGLSMGS MICGWDKKGPGLYYVDEHGTRLSGNMFSTGSGNTYAYGVMDSGYRPNLSPEEAYDLGRRA IAYATHRDSYSGGVVNMYHMKEDGWVKVESTDVSDLLHQYREANQ* Gene 6 (Forward). 15 exons. 1040 aa. Score = 51.141949 Start 116217 116219 4.46 + CCGTTGACAGAGCCATGCGG First 116217 116709 1.18 + 0 1 4.46 2.44 5.09 0.00 AA 1:165 gene_6 Donor 116709 116710 2.44 + TGGGTGAGT Acceptor 116798 116799 5.85 + TGTTATTTTTCATGCCTCTTTCAGGTG Internal 116799 116913 4.26 + 2 2 5.85 4.63 7.42 0.00 AA 165:203 gene_6 Donor 116913 116914 4.63 + CAGGTAGGT Acceptor 117436 117437 6.31 + ACTTGCTTTCCTTTCTCTTTCTAGACA Internal 117437 117484 0.05 + 1 2 6.31 3.70 -1.13 0.00 AA 203:219 gene_6 Donor 117484 117485 3.70 + GAGGTGAGC Acceptor 118676 118677 5.18 + CCCTCTTATTCTCCTACCCCACAGCTC Internal 118677 118807 3.22 + 1 1 5.18 3.05 8.20 0.00 AA 219:263 gene_6 Donor 118807 118808 3.05 + CAGGTGGGG Acceptor 119090 119091 5.08 + CCTCACCTGCTCTGTCCTTCTTAGGGG Internal 119091 119296 7.73 + 2 0 5.08 4.49 17.47 0.00 AA 263:331 gene_6 Donor 119296 119297 4.49 + CAGGTGAGC Acceptor 121625 121626 4.30 + GTGTTTGCTGGCCCTCTTTTCCAGGAA Internal 121626 121823 6.17 + 0 0 4.30 3.64 17.26 0.00 AA 332:397 gene_6 Donor 121823 121824 3.64 + AGGGTAAGA Acceptor 121988 121989 7.47 + CATCTCTTTCTTCTCCTCTTCCAGGTG Internal 121989 122117 2.09 + 0 0 7.47 4.49 1.03 0.00 AA 398:440 gene_6 Donor 122117 122118 4.49 + CAGGTGAGC Acceptor 123643 123644 4.08 + GGCTCTCCCATTCCTGTTTTCCAGACC Internal 123644 123832 2.08 + 0 0 4.08 0.30 11.14 0.00 AA 441:503 gene_6 Donor 123832 123833 0.30 + AAGGTGCCT Acceptor 124009 124010 5.53 + TTAACTCTTTTTCTGGTTTTCTAGGGG Internal 124010 124183 7.03 + 0 0 5.53 3.68 16.25 0.00 AA 504:561 gene_6 Donor 124183 124184 3.68 + CAGGTGGGT Acceptor 124360 124361 4.54 + TCTGCCCCTGTCCCTGCTGCACAGGTG Internal 124361 124520 3.46 + 0 1 4.54 1.41 12.22 0.00 AA 562:615 gene_6 Donor 124520 124521 1.41 + CAGGTATCT Acceptor 132127 132128 6.44 + GTTTTTTTTGTTTTTTTTTTCTAGAAA Internal 132128 132308 2.65 + 2 2 6.44 3.78 5.05 0.00 AA 615:675 gene_6 Donor 132308 132309 3.78 + CGGGTGAGT Acceptor 137493 137494 5.36 + ATCTCATTTTTTTCCTTTCTCCAGAAT Internal 137494 137585 1.72 + 1 1 5.36 5.38 1.95 0.00 AA 675:706 gene_6 Donor 137585 137586 5.38 + CAGGTAAGA Acceptor 139122 139123 2.30 + ATGGTTTTGGTTTTGGTTTTCCAGAAG Internal 139123 139392 4.46 + 2 1 2.30 4.31 14.99 0.00 AA 706:796 gene_6 Donor 139392 139393 4.31 + AAGGTGAGC Acceptor 139834 139835 5.08 + GTCTCATTTTTCCTCCCTTCCTAGTGC Internal 139835 140116 3.25 + 2 1 5.08 -0.18 13.27 0.00 AA 796:890 gene_6 Donor 140116 140117 -0.18 + GGAGTGAGA Acceptor 150537 150538 1.12 + AAACCCACATGATTATCTCAATAGATG Terminal 150538 150989 1.80 + 2 0 1.12 0.00 16.56 0.00 AA 890:1040 gene_6 Stop 150987 150989 0.00 + CTAG test\|geneid_v1.2_predicted_protein_6\|1040_AA MRLPDLRPWTSLLLVDAALLWLLQGPLGTLLPQGLPGLWLEGTLRLGGLWGLLKLRGLLG FVGTLLLPLCLATPLTVSLRALVAGASRAPPARVASAPWSWLLVGYGAAGLSWSLWAVLS PPGAQEKEQDQVNNKVLMWRLLKLSRPDLPLLVAAFFFLVLAVLGETLIPHYSGRVIDIL GGDFDPHAFASAIFFMCLFSFGRHTQTNKLFDKAGTGMSSLSAGCRGGCFTYTMSRINLR IREQLFSSLLRQDLGFFQETKTGELNSRLSSDTTLMSNWLPLNANVLLRSLVKVVGLYGF MLSISPRLTLLSLLHMPFTIAAEKVYNTRHQEVLREIQDAVARAGQVVREAVGGLQTVRS FGAEEHEVCRYKEALEQCRQLYWRRDLERALYLLVRRVLHLGVQMLMLSCGLQQMQDGEL TQGSLLSFMIYQESVGSYVQTLVYIYGDMLSNVGAAEKVFSYMDRQPNLPSPGTLAPTTL QGVVKFQDVSFAYPNRPDRPVLKGLTFTLRPGEVTALVGPNGSGKSTVAALLQNLYQPTG GQVLLDEKPISQYEHCYLHSQVVSVGQEPVLFSGSVRNNIAYGLQSCEDDKVMAAAQAAH ADDFIQEMEHGIYTENPLEVHDILNFSGYFLGIMSSNERICGTKHHQHLFFQDEVMDKTI TGKLRQIVHVKQYFGMGSGWVPWVVALLVNLTRLDSSMTQGTDSPEDFVIQAKADCYFTN GTEKVQFVVRFIFNLEEYVRFDSDVGMFVALTKLGQPDAEQWNSRLDLLERSRQAVDGVC RHNYRLGAPFTVGRKVQPEVTVYPERTPLLHQHNLLHCSVTGFYPGDIKIKWFLNGQEER AGVMSTGPIRNGDWTFQTVVMLEMTPELGHVYTCLVDHSSLLSPVSVEWNAEKSSDKIQH SFMLKTLDKLVIEGTYVKIVRAIYDKPAANIILNGQNLEAFPLKTGRRQECPLSLLLFNI VLEVLARAIRQEKRIKSSQIGKEEVKVFLFADDMIIYLENPIVSAQKLLKLINNFSKVSG YKINVQKLLIFLYTNNSQA* Gene 7 (Forward). 6 exons. 314 aa. Score = 20.532181 Start 159435 159437 1.25 + GAGGTGGAAAGAACATGAGG First 159435 159556 0.89 + 0 2 1.25 6.11 4.94 0.00 AA 1: 41 gene_7 Donor 159556 159557 6.11 + AAGGTAAGT Acceptor 177914 177915 5.67 + GTGCTTCCCTGTCTCTATCCCCAGGGA Internal 177915 177947 0.49 + 1 2 5.67 4.44 -0.19 0.00 AA 41: 52 gene_7 Donor 177947 177948 4.44 + CAGGTGAGA Acceptor 190045 190046 2.30 + GTATTGTGCCTTTGCTCATATCAGATG Internal 190046 190173 -1.22 + 1 1 2.30 0.25 6.88 0.00 AA 52: 95 gene_7 Donor 190173 190174 0.25 + CCAGTAGGG Acceptor 192476 192477 4.16 + CTGACCCGCCGTGATTCTCCGCAGAGG Internal 192477 192743 17.00 + 2 1 4.16 4.31 42.30 0.00 AA 95:184 gene_7 Donor 192743 192744 4.31 + AAGGTGAGC Acceptor 195268 195269 3.07 + TTCCCTGTCTGTTACTGCCCTCAGTGG Internal 195269 195550 1.81 + 2 1 3.07 1.41 11.56 0.00 AA 184:278 gene_7 Donor 195550 195551 1.41 + GGCGTAAGG Acceptor 196513 196514 2.68 + CTCACACTCAGTTCTGCTCCTTAGGGG Internal 196514 196624 1.56 + 2 1 2.68 4.53 5.59 0.00 AA 278:314 gene_7 Donor 196624 196625 4.53 + AAGGTGAGG test\|geneid_v1.2_predicted_protein_7\|314_AA MRDKSSAWPHHQQSCYYNEDEGTEKRGRDGIHQTTVLIHTRDSMTFIHLVPRCTCFMVQG GFKQLKNLQEKSQQILSLEEHECNTFLHNKESLAKDFLVQFKGMCYFTNGTERVRGVARY IYNREEYGRFDSDVGEFQAVTELGRSIEDWNNYKDFLEQERAAVDKVCRHNYEAELRTTL QRQVEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETAGVVSTSLIRNG DWTFQILVMLEITPQRGDIYTCQVEHPSLQSPITVEWRAQSESAQSKMLSGIGGFVLGLI FLGLGLIIRHRGQKag
`% bin/geneid -XP param/human3iso.param test.fa`

4. eXtended format (gff)

## gff-version 2
## date Thu Sep 27 17:28:38 2003
## source-version: geneid v 1.2 -- geneid@imim.es
## Sequence test - Length = 198285 bps
# Optimal Gene Structure. 7 genes. Score = 164.188676 
# Gene 1 (Forward). 8 exons. 525 aa. Score = 25.246988 
test  geneid_v1.2  Acceptor    3697    3698   5.39  +  .  # AACCTCACCCTGTGTCCTTTGCAGCTC
test  geneid_v1.2  Internal    3698    3982   8.69  +  2  gene_1
test  geneid_v1.2     Donor    3982    3983   1.69  +  .  # GAGGTCAGG
test  geneid_v1.2  Acceptor    4611    4612   3.01  +  .  # CCTACACTTCAATCCCCCCACCAGGGT
test  geneid_v1.2  Internal    4612    4890   5.95  +  2  gene_1
test  geneid_v1.2     Donor    4890    4891   2.36  +  .  # GGGGTGAGG
test  geneid_v1.2  Acceptor    5101    5102   0.20  +  .  # GGCTGAGCCACTCATTTCCTCCAGTAC
test  geneid_v1.2  Internal    5102    5230   1.03  +  2  gene_1
test  geneid_v1.2     Donor    5230    5231   2.06  +  .  # GTGGTATGT
test  geneid_v1.2  Acceptor   13674   13675   2.23  +  .  # ACTGAACTCCCGGCATCTTTACAGAGC
test  geneid_v1.2  Internal   13675   13737   0.26  +  2  gene_1
test  geneid_v1.2     Donor   13737   13738   5.66  +  .  # CAGGTAAGG
test  geneid_v1.2  Acceptor   15524   15525   5.61  +  .  # TTCTCCCTTCCCTGGCTCCTCTAGGTG
test  geneid_v1.2  Internal   15525   15806   4.26  +  2  gene_1
test  geneid_v1.2     Donor   15806   15807   2.81  +  .  # CACGTGAGG
test  geneid_v1.2  Acceptor   17033   17034   5.76  +  .  # AACATGTTTTTTTCTCCTATGCAGGGC
test  geneid_v1.2  Internal   17034   17318   3.80  +  2  gene_1
test  geneid_v1.2     Donor   17318   17319   1.67  +  .  # GGAGTAAGT
test  geneid_v1.2  Acceptor   21598   21599   4.61  +  .  # CTTTGTAGGTTTTTTGTTTTATAGGAA
test  geneid_v1.2  Internal   21599   21618   0.64  +  2  gene_1
test  geneid_v1.2     Donor   21618   21619   5.66  +  .  # CAGGTAAGG
test  geneid_v1.2  Acceptor   23144   23145   5.33  +  .  # CTCCCCTCTTCCCTCTGCTCTTAGGCT
test  geneid_v1.2  Terminal   23145   23375   0.61  +  0  gene_1
test  geneid_v1.2      Stop   23373   23375   0.00  +  .  # ATAG
 Gene 2 (Forward). 2 exons. 181 aa. Score = 10.263193 
test  geneid_v1.2     Start   74617   74619   5.56  +  .  # CGGAGCACCCGGCAATGGCG
test  geneid_v1.2     First   74617   74854   6.35  +  0  gene_2
test  geneid_v1.2     Donor   74854   74855  -0.98  +  .  # TGGGTGATG
test  geneid_v1.2  Acceptor   74928   74929  -6.70  +  .  # ACAGATAGCTTGCTAAGAACTTAGCTG
test  geneid_v1.2  Terminal   74929   75233   3.91  +  2  gene_2
test  geneid_v1.2      Stop   75231   75233   0.00  +  .  # ATAG
 Gene 3 (Reverse). 5 exons. 203 aa. Score = 5.699872 
test  geneid_v1.2      Stop   86249   86251   0.00  -  .  # TTGA
test  geneid_v1.2  Terminal   86249   86417   1.51  -  1  gene_3
test  geneid_v1.2  Acceptor   86417   86418   4.28  -  .  # TCGTCTCTATTTGGCCTGTTTTAGGGC
test  geneid_v1.2     Donor   94858   94859   2.22  -  .  # CTGGTATGG
test  geneid_v1.2  Internal   94859   94977  -1.65  -  0  gene_3
test  geneid_v1.2  Acceptor   94977   94978   2.55  -  .  # TCATCTACCTGGTCACTATTACAGCTG
test  geneid_v1.2     Donor   96313   96314   5.34  -  .  # CAGGTGAGT
test  geneid_v1.2  Internal   96314   96443   3.31  -  1  gene_3
test  geneid_v1.2  Acceptor   96443   96444   4.11  -  .  # CTTTATTCCTAATATTTCCCTCAGGAT
test  geneid_v1.2     Donor   97053   97054   0.34  -  .  # TGGGTATGA
test  geneid_v1.2  Internal   97054   97185   2.74  -  1  gene_3
test  geneid_v1.2  Acceptor   97185   97186   2.74  -  .  # TGACTGTTGACTCCCTCCTGACAGCGA
test  geneid_v1.2     Donor   98243   98244   3.60  -  .  # AGGGTGAGT
test  geneid_v1.2     First   98244   98302  -0.20  -  0  gene_3
test  geneid_v1.2     Start   98300   98302   1.52  -  .  # TGCAGACCACCATCATGGCA
 Gene 4 (Reverse). 1 exons. 104 aa. Score = 4.755478 
test  geneid_v1.2      Stop  100629  100631   0.00  -  .  # TTAG
test  geneid_v1.2    Single  100629  100940   4.76  -  0  gene_4
test  geneid_v1.2     Start  100938  100940   0.42  -  .  # CCAGCAGGGAGAATATGCGG
 Gene 5 (Forward). 15 exons. 766 aa. Score = 46.549015 
test  geneid_v1.2     Start  101952  101954   1.16  +  .  # TTTCTCCAGGGGAGATGGCC
test  geneid_v1.2     First  101952  102061  -1.42  +  0  gene_5
test  geneid_v1.2     Donor  102061  102062   0.34  +  .  # CAGGTCTGG
test  geneid_v1.2  Acceptor  102209  102210   4.04  +  .  # CCTTTTTTTCCGGGTTCTTTATAGTGC
test  geneid_v1.2  Internal  102210  102340  -0.15  +  1  gene_5
test  geneid_v1.2     Donor  102340  102341  -1.92  +  .  # CAGGTTTCT
test  geneid_v1.2  Acceptor  103299  103300   4.52  +  .  # ACTCTCTTCTCCCCAACCCTGCAGGTA
test  geneid_v1.2  Internal  103300  103505   3.34  +  2  gene_5
test  geneid_v1.2     Donor  103505  103506   4.14  +  .  # CAGGTATGT
test  geneid_v1.2  Acceptor  103931  103932   3.85  +  .  # CATCTCTTGTCCATGTATCCACAGTTG
test  geneid_v1.2  Internal  103932  104129   4.76  +  0  gene_5
test  geneid_v1.2     Donor  104129  104130  -0.04  +  .  # AGTGTGAGC
test  geneid_v1.2  Acceptor  105330  105331   5.35  +  .  # CCTTTTTTTGTGGTCTCTTTATAGATT
test  geneid_v1.2  Internal  105331  105459   4.56  +  0  gene_5
test  geneid_v1.2     Donor  105459  105460   3.92  +  .  # GAGGTGAGG
test  geneid_v1.2  Acceptor  105608  105609   5.64  +  .  # TTCACTATTCTTACCTCCCTCTAGGTA
test  geneid_v1.2  Internal  105609  105797   3.81  +  0  gene_5
test  geneid_v1.2     Donor  105797  105798   0.78  +  .  # CAGGTACAA
test  geneid_v1.2  Acceptor  106356  106357   3.90  +  .  # ATCGTGTGCTTCTCTGGCCTCTAGGGG
test  geneid_v1.2  Internal  106357  106530   5.45  +  0  gene_5
test  geneid_v1.2     Donor  106530  106531   3.52  +  .  # CAGGTATGG
test  geneid_v1.2  Acceptor  106773  106774   3.56  +  .  # ACTCTTCATCATATTTCATCTCAGGTG
test  geneid_v1.2  Internal  106774  106936   1.28  +  0  gene_5
test  geneid_v1.2     Donor  106936  106937   0.52  +  .  # CAGGTACTC
test  geneid_v1.2  Acceptor  107244  107245   3.85  +  .  # TCATCTTGGCCCTTTGCTCTGCAGAGG
test  geneid_v1.2  Internal  107245  107381   2.61  +  2  gene_5
test  geneid_v1.2     Donor  107381  107382   4.71  +  .  # CAGGTGAGG
test  geneid_v1.2  Acceptor  108663  108664   4.41  +  .  # TGACGGTCCGATGTCTTTCCTCAGGTG
test  geneid_v1.2  Internal  108664  108840   2.52  +  0  gene_5
test  geneid_v1.2     Donor  108840  108841  -1.36  +  .  # ATGGTGCAG
test  geneid_v1.2  Acceptor  111359  111360   4.01  +  .  # TCTCAACCTCTTTTCTCTTATCAGCCC
test  geneid_v1.2  Internal  111360  111507   1.14  +  0  gene_5
test  geneid_v1.2     Donor  111507  111508   0.44  +  .  # TTAGTGAGT
test  geneid_v1.2  Acceptor  111665  111666   4.40  +  .  # TCCCAAAGCTCCATCTTCTTCCAGGTG
test  geneid_v1.2  Internal  111666  111777   4.83  +  2  gene_5
test  geneid_v1.2     Donor  111777  111778   5.44  +  .  # CAGGTAAGC
test  geneid_v1.2  Acceptor  112185  112186   3.55  +  .  # TCACTCCACCTTGTCCTCACCCAGGCT
test  geneid_v1.2  Internal  112186  112315   4.80  +  1  gene_5
test  geneid_v1.2     Donor  112315  112316   3.50  +  .  # AAGGTGGGT
test  geneid_v1.2  Acceptor  112713  112714   2.72  +  .  # AGCCTGAAATCTTTCATCTTATAGGGT
test  geneid_v1.2  Internal  112714  112918   6.00  +  0  gene_5
test  geneid_v1.2     Donor  112918  112919   1.65  +  .  # ATAGTAAGA
test  geneid_v1.2  Acceptor  113401  113402   5.19  +  .  # TGTTCTTTTCTCATTTGTCCACAGTGT
test  geneid_v1.2  Terminal  113402  113490   3.02  +  2  gene_5
test  geneid_v1.2      Stop  113488  113490   0.00  +  .  # ATAA
 Gene 6 (Forward). 15 exons. 1040 aa. Score = 51.141949 
test  geneid_v1.2     Start  116217  116219   4.46  +  .  # CCGTTGACAGAGCCATGCGG
test  geneid_v1.2     First  116217  116709   1.18  +  0  gene_6
test  geneid_v1.2     Donor  116709  116710   2.44  +  .  # TGGGTGAGT
test  geneid_v1.2  Acceptor  116798  116799   5.85  +  .  # TGTTATTTTTCATGCCTCTTTCAGGTG
test  geneid_v1.2  Internal  116799  116913   4.26  +  2  gene_6
test  geneid_v1.2     Donor  116913  116914   4.63  +  .  # CAGGTAGGT
test  geneid_v1.2  Acceptor  117436  117437   6.31  +  .  # ACTTGCTTTCCTTTCTCTTTCTAGACA
test  geneid_v1.2  Internal  117437  117484   0.05  +  1  gene_6
test  geneid_v1.2     Donor  117484  117485   3.70  +  .  # GAGGTGAGC
test  geneid_v1.2  Acceptor  118676  118677   5.18  +  .  # CCCTCTTATTCTCCTACCCCACAGCTC
test  geneid_v1.2  Internal  118677  118807   3.22  +  1  gene_6
test  geneid_v1.2     Donor  118807  118808   3.05  +  .  # CAGGTGGGG
test  geneid_v1.2  Acceptor  119090  119091   5.08  +  .  # CCTCACCTGCTCTGTCCTTCTTAGGGG
test  geneid_v1.2  Internal  119091  119296   7.73  +  2  gene_6
test  geneid_v1.2     Donor  119296  119297   4.49  +  .  # CAGGTGAGC
test  geneid_v1.2  Acceptor  121625  121626   4.30  +  .  # GTGTTTGCTGGCCCTCTTTTCCAGGAA
test  geneid_v1.2  Internal  121626  121823   6.17  +  0  gene_6
test  geneid_v1.2     Donor  121823  121824   3.64  +  .  # AGGGTAAGA
test  geneid_v1.2  Acceptor  121988  121989   7.47  +  .  # CATCTCTTTCTTCTCCTCTTCCAGGTG
test  geneid_v1.2  Internal  121989  122117   2.09  +  0  gene_6
test  geneid_v1.2     Donor  122117  122118   4.49  +  .  # CAGGTGAGC
test  geneid_v1.2  Acceptor  123643  123644   4.08  +  .  # GGCTCTCCCATTCCTGTTTTCCAGACC
test  geneid_v1.2  Internal  123644  123832   2.08  +  0  gene_6
test  geneid_v1.2     Donor  123832  123833   0.30  +  .  # AAGGTGCCT
test  geneid_v1.2  Acceptor  124009  124010   5.53  +  .  # TTAACTCTTTTTCTGGTTTTCTAGGGG
test  geneid_v1.2  Internal  124010  124183   7.03  +  0  gene_6
test  geneid_v1.2     Donor  124183  124184   3.68  +  .  # CAGGTGGGT
test  geneid_v1.2  Acceptor  124360  124361   4.54  +  .  # TCTGCCCCTGTCCCTGCTGCACAGGTG
test  geneid_v1.2  Internal  124361  124520   3.46  +  0  gene_6
test  geneid_v1.2     Donor  124520  124521   1.41  +  .  # CAGGTATCT
test  geneid_v1.2  Acceptor  132127  132128   6.44  +  .  # GTTTTTTTTGTTTTTTTTTTCTAGAAA
test  geneid_v1.2  Internal  132128  132308   2.65  +  2  gene_6
test  geneid_v1.2     Donor  132308  132309   3.78  +  .  # CGGGTGAGT
test  geneid_v1.2  Acceptor  137493  137494   5.36  +  .  # ATCTCATTTTTTTCCTTTCTCCAGAAT
test  geneid_v1.2  Internal  137494  137585   1.72  +  1  gene_6
test  geneid_v1.2     Donor  137585  137586   5.38  +  .  # CAGGTAAGA
test  geneid_v1.2  Acceptor  139122  139123   2.30  +  .  # ATGGTTTTGGTTTTGGTTTTCCAGAAG
test  geneid_v1.2  Internal  139123  139392   4.46  +  2  gene_6
test  geneid_v1.2     Donor  139392  139393   4.31  +  .  # AAGGTGAGC
test  geneid_v1.2  Acceptor  139834  139835   5.08  +  .  # GTCTCATTTTTCCTCCCTTCCTAGTGC
test  geneid_v1.2  Internal  139835  140116   3.25  +  2  gene_6
test  geneid_v1.2     Donor  140116  140117  -0.18  +  .  # GGAGTGAGA
test  geneid_v1.2  Acceptor  150537  150538   1.12  +  .  # AAACCCACATGATTATCTCAATAGATG
test  geneid_v1.2  Terminal  150538  150989   1.80  +  2  gene_6
test  geneid_v1.2      Stop  150987  150989   0.00  +  .  # CTAG
 Gene 7 (Forward). 6 exons. 314 aa. Score = 20.532181 
test  geneid_v1.2     Start  159435  159437   1.25  +  .  # GAGGTGGAAAGAACATGAGG
test  geneid_v1.2     First  159435  159556   0.89  +  0  gene_7
test  geneid_v1.2     Donor  159556  159557   6.11  +  .  # AAGGTAAGT
test  geneid_v1.2  Acceptor  177914  177915   5.67  +  .  # GTGCTTCCCTGTCTCTATCCCCAGGGA
test  geneid_v1.2  Internal  177915  177947   0.49  +  1  gene_7
test  geneid_v1.2     Donor  177947  177948   4.44  +  .  # CAGGTGAGA
test  geneid_v1.2  Acceptor  190045  190046   2.30  +  .  # GTATTGTGCCTTTGCTCATATCAGATG
test  geneid_v1.2  Internal  190046  190173  -1.22  +  1  gene_7
test  geneid_v1.2     Donor  190173  190174   0.25  +  .  # CCAGTAGGG
test  geneid_v1.2  Acceptor  192476  192477   4.16  +  .  # CTGACCCGCCGTGATTCTCCGCAGAGG
test  geneid_v1.2  Internal  192477  192743  17.00  +  2  gene_7
test  geneid_v1.2     Donor  192743  192744   4.31  +  .  # AAGGTGAGC
test  geneid_v1.2  Acceptor  195268  195269   3.07  +  .  # TTCCCTGTCTGTTACTGCCCTCAGTGG
test  geneid_v1.2  Internal  195269  195550   1.81  +  2  gene_7
test  geneid_v1.2     Donor  195550  195551   1.41  +  .  # GGCGTAAGG
test  geneid_v1.2  Acceptor  196513  196514   2.68  +  .  # CTCACACTCAGTTCTGCTCCTTAGGGG
test  geneid_v1.2  Internal  196514  196624   1.56  +  2  gene_7
test  geneid_v1.2     Donor  196624  196625   4.53  +  .  # AAGGTGAGG

% bin/geneid -XGP param/human3iso.param test.fa

5. XML Format

5. XML format

<?xml version="1.0" ?>
<!DOCTYPE prediction SYSTEM "geneid.dtd">
<prediction locus="test" length="198285" source="geneid_v1.2" 
date="Thu Sep 27 17:44:50 2003" genes="7" score ="164.19">
   <gene idGene="test.G1" strand ="fwd" exons="8" score="25.25">
      <exon idExon="test.G1E1" type="Internal" frame="2" score="8.69">
         <site idSite="test.G1E1S1" type="Acceptor" position="3698" score="5.39" />
         <site idSite="test.G1E1S2" type="Donor" position="3982" score="1.69" />
      </exon>
      <exon idExon="test.G1E2" type="Internal" frame="2" score="5.95">
         <site idSite="test.G1E2S1" type="Acceptor" position="4612" score="3.01" />
         <site idSite="test.G1E2S2" type="Donor" position="4890" score="2.36" />
      </exon>
      <exon idExon="test.G1E3" type="Internal" frame="2" score="1.03">
         <site idSite="test.G1E3S1" type="Acceptor" position="5102" score="0.20" />
         <site idSite="test.G1E3S2" type="Donor" position="5230" score="2.06" />
      </exon>
      <exon idExon="test.G1E4" type="Internal" frame="2" score="0.26">
         <site idSite="test.G1E4S1" type="Acceptor" position="13675" score="2.23" />
         <site idSite="test.G1E4S2" type="Donor" position="13737" score="5.66" />
      </exon>
      <exon idExon="test.G1E5" type="Internal" frame="2" score="4.26">
         <site idSite="test.G1E5S1" type="Acceptor" position="15525" score="5.61" />
         <site idSite="test.G1E5S2" type="Donor" position="15806" score="2.81" />
      </exon>
      <exon idExon="test.G1E6" type="Internal" frame="2" score="3.80">
         <site idSite="test.G1E6S1" type="Acceptor" position="17034" score="5.76" />
         <site idSite="test.G1E6S2" type="Donor" position="17318" score="1.67" />
      </exon>
      <exon idExon="test.G1E7" type="Internal" frame="2" score="0.64">
         <site idSite="test.G1E7S1" type="Acceptor" position="21599" score="4.61" />
         <site idSite="test.G1E7S2" type="Donor" position="21618" score="5.66" />
      </exon>
      <exon idExon="test.G1E8" type="Terminal" frame="0" score="0.61">
         <site idSite="test.G1E8S1" type="Acceptor" position="23145" score="5.33" />
         <site idSite="test.G1E8S2" type="Stop" position="23375" score="0.00" />
      </exon>
      <protein length="525">
	ctPTPMWPDDLQNHTFLHTVYCQDGSPSVGLSEAYDEDQLFFFDFSQNTRVPRLPEFADW
	AQEQGDAPAILFDKEFCEWMIQQIGPKLDGKIPVSRGFPIAEVFTLKPLEFGKPNTLVCF
	VSNLFPPMLTVNWQHHSVPVEGFGPTFVSAVDGLSFQAFSYLNFTPEPSDIFSCIVTHEI
	DRYTAIAYWVPRNALPSDLLENVLCGVAFGLGVLGIIVGIVLIIYFRKPCSGEQSMITFL
	PLLLGLSLGCTGAGGFVAHVESTCLLDDAGTPKDFTYCISFNKDLLTCWDPEENKMAPCE
	FGVLNSLANVLSQHLNQKDTLMQRLRNGLQNCATHTQPFWGSLTNRTRPPSVQVAKTTPF
	NTREPVMLACYVWGFYPAEVTITWRKNGKLVMPHSSAHKTAQPNGDWTYQTLSHLALTPS
	YGDTYTCVVEHIGAPEPILRDWRKAVPFQADAGSKKKPGSMGAIQCHAGQHLRQTPGAEV
	LRVGPEGQMEDRKYIHNKKEKRQCCGVEREVQNLGFFWPWTMTSA*
      </protein>
   </gene>
   <gene idGene="test.G2" strand ="fwd" exons="2" score="10.26">
      <exon idExon="test.G2E1" type="First" frame="0" score="6.35">
         <site idSite="test.G2E1S1" type="Start" position="74617" score="5.56" />
         <site idSite="test.G2E1S2" type="Donor" position="74854" score="-0.98" />
      </exon>
      <exon idExon="test.G2E2" type="Terminal" frame="2" score="3.91">
         <site idSite="test.G2E2S1" type="Acceptor" position="74929" score="-6.70" />
         <site idSite="test.G2E2S2" type="Stop" position="75233" score="0.00" />
      </exon>
      <protein length="181">
	MAASTASQRPLKGILKDNTSTTSSMVASAEHPRGSVHEQLSKKSQKWDEMNILATYRPAD
	KDYGLMKIDEPSTPYHSTMAAAEGLEPKYQVQEQESSGEEDSDLSPEEREKKRQFEMRRT
	LHYNEGLNIKLARQLISKDLHDDDKVEEMLETAHGESMNTEESNQGSTASDQQQNKSRSS
	*
      </protein>
   </gene>
   <gene idGene="test.G3" strand ="rvs" exons="5" score="5.70">
      <exon idExon="test.G3E1" type="Terminal" frame="1" score="1.51">
         <site idSite="test.G3E1S1" type="Stop" position="86249" score="0.00" />
         <site idSite="test.G3E1S2" type="Acceptor" position="86417" score="4.28" />
      </exon>
      <exon idExon="test.G3E2" type="Internal" frame="0" score="-1.65">
         <site idSite="test.G3E2S1" type="Donor" position="94859" score="2.22" />
         <site idSite="test.G3E2S2" type="Acceptor" position="94977" score="2.55" />
      </exon>
      <exon idExon="test.G3E3" type="Internal" frame="1" score="3.31">
         <site idSite="test.G3E3S1" type="Donor" position="96314" score="5.34" />
         <site idSite="test.G3E3S2" type="Acceptor" position="96443" score="4.11" />
      </exon>
      <exon idExon="test.G3E4" type="Internal" frame="1" score="2.74">
         <site idSite="test.G3E4S1" type="Donor" position="97054" score="0.34" />
         <site idSite="test.G3E4S2" type="Acceptor" position="97185" score="2.74" />
      </exon>
      <exon idExon="test.G3E5" type="First" frame="0" score="-0.20">
         <site idSite="test.G3E5S1" type="Donor" position="98244" score="3.60" />
         <site idSite="test.G3E5S2" type="Start" position="98302" score="1.52" />
      </exon>
      <protein length="203">
	MAVEFDGGVVMGSDSRVSAGEAVVNRVFDKLSPLHERIYCALSGSAADAQAVADMAAYQL
	ELHGIELEEPPLVLAAANVVRNISYKYREDLSAHLMVAGWDQREGGQLPVWTIESSWAMN
	CQNSMMSEPSPDFSFLFCNKLSRAKTWAKPRSKIFFKMNVLTVTMPDLEYEQEHPFTLTE
	TYVVTKTYINNIFNLDKINLEN*
      </protein>
   </gene>
   <gene idGene="test.G4" strand ="rvs" exons="1" score="4.76">
      <exon idExon="test.G4E1" type="Single" frame="0" score="4.76">
         <site idSite="test.G4E1S1" type="Stop" position="100629" score="0.00" />
         <site idSite="test.G4E1S2" type="Start" position="100940" score="0.42" />
      </exon>
      <protein length="104">
	MRGSAVRSSTQSARSSSTVPSHAREAPGRQRHPRGAGHLELAIGTRTPSRSRPGLGLSAP
	RWGLKLRVPPSPPLLAAGGGNEGGALGKSQEQADPALARSSAI*
      </protein>
   </gene>
   <gene idGene="test.G5" strand ="fwd" exons="15" score="46.55">
      <exon idExon="test.G5E1" type="First" frame="0" score="-1.42">
         <site idSite="test.G5E1S1" type="Start" position="101952" score="1.16" />
         <site idSite="test.G5E1S2" type="Donor" position="102061" score="0.34" />
      </exon>
      <exon idExon="test.G5E2" type="Internal" frame="1" score="-0.15">
         <site idSite="test.G5E2S1" type="Acceptor" position="102210" score="4.04" />
         <site idSite="test.G5E2S2" type="Donor" position="102340" score="-1.92" />
      </exon>
      <exon idExon="test.G5E3" type="Internal" frame="2" score="3.34">
         <site idSite="test.G5E3S1" type="Acceptor" position="103300" score="4.52" />
         <site idSite="test.G5E3S2" type="Donor" position="103505" score="4.14" />
      </exon>
      <exon idExon="test.G5E4" type="Internal" frame="0" score="4.76">
         <site idSite="test.G5E4S1" type="Acceptor" position="103932" score="3.85" />
         <site idSite="test.G5E4S2" type="Donor" position="104129" score="-0.04" />
      </exon>
      <exon idExon="test.G5E5" type="Internal" frame="0" score="4.56">
         <site idSite="test.G5E5S1" type="Acceptor" position="105331" score="5.35" />
         <site idSite="test.G5E5S2" type="Donor" position="105459" score="3.92" />
      </exon>
      <exon idExon="test.G5E6" type="Internal" frame="0" score="3.81">
         <site idSite="test.G5E6S1" type="Acceptor" position="105609" score="5.64" />
         <site idSite="test.G5E6S2" type="Donor" position="105797" score="0.78" />
      </exon>
      <exon idExon="test.G5E7" type="Internal" frame="0" score="5.45">
         <site idSite="test.G5E7S1" type="Acceptor" position="106357" score="3.90" />
         <site idSite="test.G5E7S2" type="Donor" position="106530" score="3.52" />
      </exon>
      <exon idExon="test.G5E8" type="Internal" frame="0" score="1.28">
         <site idSite="test.G5E8S1" type="Acceptor" position="106774" score="3.56" />
         <site idSite="test.G5E8S2" type="Donor" position="106936" score="0.52" />
      </exon>
      <exon idExon="test.G5E9" type="Internal" frame="2" score="2.61">
         <site idSite="test.G5E9S1" type="Acceptor" position="107245" score="3.85" />
         <site idSite="test.G5E9S2" type="Donor" position="107381" score="4.71" />
      </exon>
      <exon idExon="test.G5E10" type="Internal" frame="0" score="2.52">
         <site idSite="test.G5E10S1" type="Acceptor" position="108664" score="4.41" />
         <site idSite="test.G5E10S2" type="Donor" position="108840" score="-1.36" />
      </exon>
      <exon idExon="test.G5E11" type="Internal" frame="0" score="1.14">
         <site idSite="test.G5E11S1" type="Acceptor" position="111360" score="4.01" />
         <site idSite="test.G5E11S2" type="Donor" position="111507" score="0.44" />
      </exon>
      <exon idExon="test.G5E12" type="Internal" frame="2" score="4.83">
         <site idSite="test.G5E12S1" type="Acceptor" position="111666" score="4.40" />
         <site idSite="test.G5E12S2" type="Donor" position="111777" score="5.44" />
      </exon>
      <exon idExon="test.G5E13" type="Internal" frame="1" score="4.80">
         <site idSite="test.G5E13S1" type="Acceptor" position="112186" score="3.55" />
         <site idSite="test.G5E13S2" type="Donor" position="112315" score="3.50" />
      </exon>
      <exon idExon="test.G5E14" type="Internal" frame="0" score="6.00">
         <site idSite="test.G5E14S1" type="Acceptor" position="112714" score="2.72" />
         <site idSite="test.G5E14S2" type="Donor" position="112918" score="1.65" />
      </exon>
      <exon idExon="test.G5E15" type="Terminal" frame="2" score="3.02">
         <site idSite="test.G5E15S1" type="Acceptor" position="113402" score="5.19" />
         <site idSite="test.G5E15S2" type="Stop" position="113490" score="0.00" />
      </exon>
      <protein length="766">
	MAIPFFTGRLTDWILQDGSADTFTRNLTLMSILTIASAVLEFVGDGIYNNTMGHVHSHLQ
	GEVFGAVLRQETEFFQQNQTGNIMSRVTEDTSTLSDSLSENLSLFLWYLVRGLCLLGIML
	WGSVSLTMVTLITLPLLFLLPKKVGKWYQLLEVQVRESLAKSSQVAIEALSAMPTVRSFA
	NEEGEAQKFREKLQEIKTLNQKEAVAYAVNSWTTSISGMLLKVGILYIGGQLVTSGAVSS
	GNLVTFVLYQMQFTQAVEVLLSIYPRVQKAVGSSEKIFEYLDRTPRCPPSGLLTPLHLEG
	LVQFQDVSFAYPNRPDVLVLQGLTFTLRPGEVTALVGPNGSGKSTVAALLQNLYQPTGGQ
	LLLDGKPLPQYEHRYLHRQVAAVGQEPQVFGRSLQENIAYGLTQKPTMEEITAAAVKSGA
	HSFISGLPQGYDTEVDEAGSQLSGGQRQAVALARALIRKPCVLILDDATSALDANSQLQV
	EQLLYESPERYSRSVLLITQHLSLVEQADHILFLEGGAIREGGTHQQLMEKKGCYWAMPT
	EFFQSLGGDGERNVQIEMAHGTTTLAFKFQHGVIAAVDSRASAGSYISALRVNKVIEINP
	YLLGTMSGCAADCQYWERLLAKECRLYYLRNGERISVSAASKLLSNMMCQYRGMGLSMGS
	MICGWDKKGPGLYYVDEHGTRLSGNMFSTGSGNTYAYGVMDSGYRPNLSPEEAYDLGRRA
	IAYATHRDSYSGGVVNMYHMKEDGWVKVESTDVSDLLHQYREANQ*
      </protein>
   </gene>
   <gene idGene="test.G6" strand ="fwd" exons="15" score="51.14">
      <exon idExon="test.G6E1" type="First" frame="0" score="1.18">
         <site idSite="test.G6E1S1" type="Start" position="116217" score="4.46" />
         <site idSite="test.G6E1S2" type="Donor" position="116709" score="2.44" />
      </exon>
      <exon idExon="test.G6E2" type="Internal" frame="2" score="4.26">
         <site idSite="test.G6E2S1" type="Acceptor" position="116799" score="5.85" />
         <site idSite="test.G6E2S2" type="Donor" position="116913" score="4.63" />
      </exon>
      <exon idExon="test.G6E3" type="Internal" frame="1" score="0.05">
         <site idSite="test.G6E3S1" type="Acceptor" position="117437" score="6.31" />
         <site idSite="test.G6E3S2" type="Donor" position="117484" score="3.70" />
      </exon>
      <exon idExon="test.G6E4" type="Internal" frame="1" score="3.22">
         <site idSite="test.G6E4S1" type="Acceptor" position="118677" score="5.18" />
         <site idSite="test.G6E4S2" type="Donor" position="118807" score="3.05" />
      </exon>
      <exon idExon="test.G6E5" type="Internal" frame="2" score="7.73">
         <site idSite="test.G6E5S1" type="Acceptor" position="119091" score="5.08" />
         <site idSite="test.G6E5S2" type="Donor" position="119296" score="4.49" />
      </exon>
      <exon idExon="test.G6E6" type="Internal" frame="0" score="6.17">
         <site idSite="test.G6E6S1" type="Acceptor" position="121626" score="4.30" />
         <site idSite="test.G6E6S2" type="Donor" position="121823" score="3.64" />
      </exon>
      <exon idExon="test.G6E7" type="Internal" frame="0" score="2.09">
         <site idSite="test.G6E7S1" type="Acceptor" position="121989" score="7.47" />
         <site idSite="test.G6E7S2" type="Donor" position="122117" score="4.49" />
      </exon>
      <exon idExon="test.G6E8" type="Internal" frame="0" score="2.08">
         <site idSite="test.G6E8S1" type="Acceptor" position="123644" score="4.08" />
         <site idSite="test.G6E8S2" type="Donor" position="123832" score="0.30" />
      </exon>
      <exon idExon="test.G6E9" type="Internal" frame="0" score="7.03">
         <site idSite="test.G6E9S1" type="Acceptor" position="124010" score="5.53" />
         <site idSite="test.G6E9S2" type="Donor" position="124183" score="3.68" />
      </exon>
      <exon idExon="test.G6E10" type="Internal" frame="0" score="3.46">
         <site idSite="test.G6E10S1" type="Acceptor" position="124361" score="4.54" />
         <site idSite="test.G6E10S2" type="Donor" position="124520" score="1.41" />
      </exon>
      <exon idExon="test.G6E11" type="Internal" frame="2" score="2.65">
         <site idSite="test.G6E11S1" type="Acceptor" position="132128" score="6.44" />
         <site idSite="test.G6E11S2" type="Donor" position="132308" score="3.78" />
      </exon>
      <exon idExon="test.G6E12" type="Internal" frame="1" score="1.72">
         <site idSite="test.G6E12S1" type="Acceptor" position="137494" score="5.36" />
         <site idSite="test.G6E12S2" type="Donor" position="137585" score="5.38" />
      </exon>
      <exon idExon="test.G6E13" type="Internal" frame="2" score="4.46">
         <site idSite="test.G6E13S1" type="Acceptor" position="139123" score="2.30" />
         <site idSite="test.G6E13S2" type="Donor" position="139392" score="4.31" />
      </exon>
      <exon idExon="test.G6E14" type="Internal" frame="2" score="3.25">
         <site idSite="test.G6E14S1" type="Acceptor" position="139835" score="5.08" />
         <site idSite="test.G6E14S2" type="Donor" position="140116" score="-0.18" />
      </exon>
      <exon idExon="test.G6E15" type="Terminal" frame="2" score="1.80">
         <site idSite="test.G6E15S1" type="Acceptor" position="150538" score="1.12" />
         <site idSite="test.G6E15S2" type="Stop" position="150989" score="0.00" />
      </exon>
      <protein length="1040">
	MRLPDLRPWTSLLLVDAALLWLLQGPLGTLLPQGLPGLWLEGTLRLGGLWGLLKLRGLLG
	FVGTLLLPLCLATPLTVSLRALVAGASRAPPARVASAPWSWLLVGYGAAGLSWSLWAVLS
	PPGAQEKEQDQVNNKVLMWRLLKLSRPDLPLLVAAFFFLVLAVLGETLIPHYSGRVIDIL
	GGDFDPHAFASAIFFMCLFSFGRHTQTNKLFDKAGTGMSSLSAGCRGGCFTYTMSRINLR
	IREQLFSSLLRQDLGFFQETKTGELNSRLSSDTTLMSNWLPLNANVLLRSLVKVVGLYGF
	MLSISPRLTLLSLLHMPFTIAAEKVYNTRHQEVLREIQDAVARAGQVVREAVGGLQTVRS
	FGAEEHEVCRYKEALEQCRQLYWRRDLERALYLLVRRVLHLGVQMLMLSCGLQQMQDGEL
	TQGSLLSFMIYQESVGSYVQTLVYIYGDMLSNVGAAEKVFSYMDRQPNLPSPGTLAPTTL
	QGVVKFQDVSFAYPNRPDRPVLKGLTFTLRPGEVTALVGPNGSGKSTVAALLQNLYQPTG
	GQVLLDEKPISQYEHCYLHSQVVSVGQEPVLFSGSVRNNIAYGLQSCEDDKVMAAAQAAH
	ADDFIQEMEHGIYTENPLEVHDILNFSGYFLGIMSSNERICGTKHHQHLFFQDEVMDKTI
	TGKLRQIVHVKQYFGMGSGWVPWVVALLVNLTRLDSSMTQGTDSPEDFVIQAKADCYFTN
	GTEKVQFVVRFIFNLEEYVRFDSDVGMFVALTKLGQPDAEQWNSRLDLLERSRQAVDGVC
	RHNYRLGAPFTVGRKVQPEVTVYPERTPLLHQHNLLHCSVTGFYPGDIKIKWFLNGQEER
	AGVMSTGPIRNGDWTFQTVVMLEMTPELGHVYTCLVDHSSLLSPVSVEWNAEKSSDKIQH
	SFMLKTLDKLVIEGTYVKIVRAIYDKPAANIILNGQNLEAFPLKTGRRQECPLSLLLFNI
	VLEVLARAIRQEKRIKSSQIGKEEVKVFLFADDMIIYLENPIVSAQKLLKLINNFSKVSG
	YKINVQKLLIFLYTNNSQA*
      </protein>
   </gene>
   <gene idGene="test.G7" strand ="fwd" exons="6" score="20.53">
      <exon idExon="test.G7E1" type="First" frame="0" score="0.89">
         <site idSite="test.G7E1S1" type="Start" position="159435" score="1.25" />
         <site idSite="test.G7E1S2" type="Donor" position="159556" score="6.11" />
      </exon>
      <exon idExon="test.G7E2" type="Internal" frame="1" score="0.49">
         <site idSite="test.G7E2S1" type="Acceptor" position="177915" score="5.67" />
         <site idSite="test.G7E2S2" type="Donor" position="177947" score="4.44" />
      </exon>
      <exon idExon="test.G7E3" type="Internal" frame="1" score="-1.22">
         <site idSite="test.G7E3S1" type="Acceptor" position="190046" score="2.30" />
         <site idSite="test.G7E3S2" type="Donor" position="190173" score="0.25" />
      </exon>
      <exon idExon="test.G7E4" type="Internal" frame="2" score="17.00">
         <site idSite="test.G7E4S1" type="Acceptor" position="192477" score="4.16" />
         <site idSite="test.G7E4S2" type="Donor" position="192743" score="4.31" />
      </exon>
      <exon idExon="test.G7E5" type="Internal" frame="2" score="1.81">
         <site idSite="test.G7E5S1" type="Acceptor" position="195269" score="3.07" />
         <site idSite="test.G7E5S2" type="Donor" position="195550" score="1.41" />
      </exon>
      <exon idExon="test.G7E6" type="Internal" frame="2" score="1.56">
         <site idSite="test.G7E6S1" type="Acceptor" position="196514" score="2.68" />
         <site idSite="test.G7E6S2" type="Donor" position="196624" score="4.53" />
      </exon>
      <protein length="314">
	MRDKSSAWPHHQQSCYYNEDEGTEKRGRDGIHQTTVLIHTRDSMTFIHLVPRCTCFMVQG
	GFKQLKNLQEKSQQILSLEEHECNTFLHNKESLAKDFLVQFKGMCYFTNGTERVRGVARY
	IYNREEYGRFDSDVGEFQAVTELGRSIEDWNNYKDFLEQERAAVDKVCRHNYEAELRTTL
	QRQVEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETAGVVSTSLIRNG
	DWTFQILVMLEITPQRGDIYTCQVEHPSLQSPITVEWRAQSESAQSKMLSGIGGFVLGLI
	FLGLGLIIRHRGQKag
      </protein>
   </gene>
</prediction>

% bin/geneid -MP param/human3iso.param test.fa

- Geneid samples re annotation

geneid samples: re-annotation

1. Prediction ab initio

## gff-version 2 ## date Thu Jul 5 11:05:29 2003 ## source-version: geneid v 1.1 -- geneid@imim.es ## Sequence cons.x8bisXs.970911 - Length = 151676 bps # Optimal Gene Structure. 7 genes. Score = 106.865317 # Gene 1 (Reverse). 11 exons. 618 aa. Score = 35.850634 cons.x8bisXs.970911 geneid_v1.2 Internal 4001 4150 0.31 - 2 gene_1 cons.x8bisXs.970911 geneid_v1.2 Internal 4515 4905 2.36 - 0 gene_1 cons.x8bisXs.970911 geneid_v1.2 Internal 5514 5750 1.36 - 0 gene_1 cons.x8bisXs.970911 geneid_v1.2 Internal 7504 7569 1.77 - 0 gene_1 cons.x8bisXs.970911 geneid_v1.2 Internal 7909 8116 7.21 - 1 gene_1 cons.x8bisXs.970911 geneid_v1.2 Internal 8421 8506 1.30 - 0 gene_1 cons.x8bisXs.970911 geneid_v1.2 Internal 9478 9592 5.78 - 1 gene_1 cons.x8bisXs.970911 geneid_v1.2 Internal 9763 9955 0.18 - 2 gene_1 cons.x8bisXs.970911 geneid_v1.2 Internal 10669 10770 1.74 - 2 gene_1 cons.x8bisXs.970911 geneid_v1.2 Internal 10903 11070 7.45 - 2 gene_1 cons.x8bisXs.970911 geneid_v1.2 First 11149 11284 6.41 - 0 gene_1 # Gene 2 (Reverse). 3 exons. 493 aa. Score = 25.252512 cons.x8bisXs.970911 geneid_v1.2 Terminal 21839 22922 18.37 - 1 gene_2 cons.x8bisXs.970911 geneid_v1.2 Internal 23679 24029 7.99 - 1 gene_2 cons.x8bisXs.970911 geneid_v1.2 First 30732 30775 -1.11 - 0 gene_2 # Gene 3 (Forward). 1 exons. 77 aa. Score = 1.009624 cons.x8bisXs.970911 geneid_v1.2 Single 31465 31695 1.01 + 0 gene_3 # Gene 4 (Reverse). 1 exons. 64 aa. Score = 0.612301 cons.x8bisXs.970911 geneid_v1.2 Single 48468 48659 0.61 - 0 gene_4 # Gene 5 (Forward). 6 exons. 220 aa. Score = 0.610088 cons.x8bisXs.970911 geneid_v1.2 First 53124 53261 0.33 + 0 gene_5 cons.x8bisXs.970911 geneid_v1.2 Internal 87535 87599 -0.78 + 0 gene_5 cons.x8bisXs.970911 geneid_v1.2 Internal 97769 97942 0.66 + 1 gene_5 cons.x8bisXs.970911 geneid_v1.2 Internal 100189 100281 0.85 + 1 gene_5 cons.x8bisXs.970911 geneid_v1.2 Internal 109098 109228 -1.00 + 1 gene_5 cons.x8bisXs.970911 geneid_v1.2 Terminal 112987 113045 0.55 + 2 gene_5 # Gene 6 (Reverse). 2 exons. 84 aa. Score = 1.237887 cons.x8bisXs.970911 geneid_v1.2 Terminal 113700 113816 -0.15 - 0 gene_6 cons.x8bisXs.970911 geneid_v1.2 First 114104 114238 1.38 - 0 gene_6 # Gene 7 (Forward). 6 exons. 365 aa. Score = 42.292270 cons.x8bisXs.970911 geneid_v1.2 First 135780 135891 2.76 + 0 gene_7 cons.x8bisXs.970911 geneid_v1.2 Internal 142150 142446 14.69 + 2 gene_7 cons.x8bisXs.970911 geneid_v1.2 Internal 144435 144603 5.04 + 2 gene_7 cons.x8bisXs.970911 geneid_v1.2 Internal 146071 146236 5.28 + 1 gene_7 cons.x8bisXs.970911 geneid_v1.2 Internal 147791 148030 12.98 + 0 gene_7 cons.x8bisXs.970911 geneid_v1.2 Terminal 150313 150423 1.53 + 0 gene_7

% geneid -G test.fasta

2. Introducing evidences (without group)

## Annotated gene cons.x8bisXs.970911 annotation Terminal 11190 11300 . - . cons.x8bisXs.970911 annotation Internal 21842 22922 . - . cons.x8bisXs.970911 annotation Internal 23679 24029 . - . cons.x8bisXs.970911 annotation Internal 30732 30772 . - . cons.x8bisXs.970911 annotation Internal 48471 48659 . - . cons.x8bisXs.970911 annotation First 52780 52800 . - .


## gff-version 2
## date Thu Jul  5 11:27:58 2003
## source-version: geneid v 1.1 -- geneid@imim.es
## Sequence cons.x8bisXs.970911 - Length = 151676 bps
# Optimal Gene Structure. 5 genes. Score = 65.815047 
# Gene 1 (Reverse). 9 exons. 453 aa. Score = 20.329739 
cons.x8bisXs.970911  geneid_v1.2 Internal   4001     4150    0.31 -  2  gene_1
cons.x8bisXs.970911  geneid_v1.2 Internal   4515     4905    2.36 -  0  gene_1
cons.x8bisXs.970911  geneid_v1.2 Internal   5514     5750    1.36 -  0  gene_1
cons.x8bisXs.970911  geneid_v1.2 Internal   7504     7569    1.77 -  0  gene_1
cons.x8bisXs.970911  geneid_v1.2 Internal   7909     8116    7.21 -  1  gene_1
cons.x8bisXs.970911  geneid_v1.2 Internal   8421     8506    1.30 -  0  gene_1
cons.x8bisXs.970911  geneid_v1.2 Internal   9478     9592    5.78 -  1  gene_1
cons.x8bisXs.970911  geneid_v1.2 Internal   9763     9827   -0.77 -  0  gene_1
cons.x8bisXs.970911  geneid_v1.2 First     10071    10109    1.03 -  0  gene_1
# Gene 2 (Reverse). 2 exons. 60 aa. Score = 1.938525 
cons.x8bisXs.970911  evidence    Terminal  11190    11300    0.00 -  0  gene_2
cons.x8bisXs.970911  geneid_v1.2 First     11377    11445    1.94 -  0  gene_2
# Gene 3 (Reverse). 6 exons. 599 aa. Score = 0.016626 
cons.x8bisXs.970911  geneid_v1.2 Terminal  13926    14039    0.02 -  0  gene_3
cons.x8bisXs.970911  evidence    Internal  21842    22922    0.00 -  1  gene_3
cons.x8bisXs.970911  evidence    Internal  23679    24029    0.00 -  1  gene_3
cons.x8bisXs.970911  evidence    Internal  30732    30772    0.00 -  0  gene_3
cons.x8bisXs.970911  evidence    Internal  48471    48659    0.00 -  0  gene_3
cons.x8bisXs.970911  evidence    First     52780    52800    0.00 -  0  gene_3
# Gene 4 (Reverse). 2 exons. 84 aa. Score = 1.237887 
cons.x8bisXs.970911  geneid_v1.2 Terminal 113700   113816   -0.15 -  0  gene_4
cons.x8bisXs.970911  geneid_v1.2 First    114104   114238    1.38 -  0  gene_4
# Gene 5 (Forward). 6 exons. 365 aa. Score = 42.292270 
cons.x8bisXs.970911  geneid_v1.2 First    135780   135891    2.76 +  0  gene_5
cons.x8bisXs.970911  geneid_v1.2 Internal 142150   142446   14.69 +  2  gene_5
cons.x8bisXs.970911  geneid_v1.2 Internal 144435   144603    5.04 +  2  gene_5
cons.x8bisXs.970911  geneid_v1.2 Internal 146071   146236    5.28 +  1  gene_5
cons.x8bisXs.970911  geneid_v1.2 Internal 147791   148030   12.98 +  0  gene_5
cons.x8bisXs.970911  geneid_v1.2 Terminal 150313   150423    1.53 +  0  gene_5

% geneid -GR evi.gff test.fasta

3. Introducing evidences (with group)

## Annotated gene cons.x8bisXs.970911 annotation Terminal 11190 11300 . - . id_x cons.x8bisXs.970911 annotation Internal 21842 22922 . - . id_x cons.x8bisXs.970911 annotation Internal 23679 24029 . - . id_x cons.x8bisXs.970911 annotation Internal 30732 30772 . - . id_x cons.x8bisXs.970911 annotation Internal 48471 48659 . - . id_x cons.x8bisXs.970911 annotation First 52780 52800 . - . id_x

## gff-version 2 ## date Thu Jul 5 11:28:29 2003 ## source-version: geneid v 1.1 -- geneid@imim.es ## Sequence cons.x8bisXs.970911 - Length = 151676 bps # Optimal Gene Structure. 4 genes. Score = 63.859896 # Gene 1 (Reverse). 9 exons. 453 aa. Score = 20.329739 cons.x8bisXs.970911 geneid_v1.2 Internal 4001 4150 0.31 - 2 gene_1 cons.x8bisXs.970911 geneid_v1.2 Internal 4515 4905 2.36 - 0 gene_1 cons.x8bisXs.970911 geneid_v1.2 Internal 5514 5750 1.36 - 0 gene_1 cons.x8bisXs.970911 geneid_v1.2 Internal 7504 7569 1.77 - 0 gene_1 cons.x8bisXs.970911 geneid_v1.2 Internal 7909 8116 7.21 - 1 gene_1 cons.x8bisXs.970911 geneid_v1.2 Internal 8421 8506 1.30 - 0 gene_1 cons.x8bisXs.970911 geneid_v1.2 Internal 9478 9592 5.78 - 1 gene_1 cons.x8bisXs.970911 geneid_v1.2 Internal 9763 9827 -0.77 - 0 gene_1 cons.x8bisXs.970911 geneid_v1.2 First 10071 10109 1.03 - 0 gene_1 # Gene 2 (Reverse). 6 exons. 598 aa. Score = 0.000000 cons.x8bisXs.970911 evidence Terminal 11190 11300 0.00 - 0 gene_2 cons.x8bisXs.970911 evidence Internal 21842 22922 0.00 - 1 gene_2 cons.x8bisXs.970911 evidence Internal 23679 24029 0.00 - 1 gene_2 cons.x8bisXs.970911 evidence Internal 30732 30772 0.00 - 0 gene_2 cons.x8bisXs.970911 evidence Internal 48471 48659 0.00 - 0 gene_2 cons.x8bisXs.970911 evidence First 52780 52800 0.00 - 0 gene_2 # Gene 3 (Reverse). 2 exons. 84 aa. Score = 1.237887 cons.x8bisXs.970911 geneid_v1.2 Terminal 113700 113816 -0.15 - 0 gene_3 cons.x8bisXs.970911 geneid_v1.2 First 114104 114238 1.38 - 0 gene_3 # Gene 4 (Forward). 6 exons. 365 aa. Score = 42.292270 cons.x8bisXs.970911 geneid_v1.2 First 135780 135891 2.76 + 0 gene_4 cons.x8bisXs.970911 geneid_v1.2 Internal 142150 142446 14.69 + 2 gene_4 cons.x8bisXs.970911 geneid_v1.2 Internal 144435 144603 5.04 + 2 gene_4 cons.x8bisXs.970911 geneid_v1.2 Internal 146071 146236 5.28 + 1 gene_4 cons.x8bisXs.970911 geneid_v1.2 Internal 147791 148030 12.98 + 0 gene_4 cons.x8bisXs.970911 geneid_v1.2 Terminal 150313 150423 1.53 + 0 gene_4

% geneid -GR evi.gff test.fasta

- Geneid samples homology information

geneid samples: homology information

1. Prediction ab initio

## gff-version 2 ## date Mon Oct 8 09:48:32 2003 ## source-version: geneid v 1.2 -- geneid@imim.es ## Sequence test - Length = 198285 bps # Optimal Gene Structure. 6 genes. Score = 161.724069 Gene 1 (Forward). 8 exons. 525 aa. Score = 25.246988 test geneid_v1.2 Internal 3698 3982 8.69 + 2 gene_1 test geneid_v1.2 Internal 4612 4890 5.95 + 2 gene_1 test geneid_v1.2 Internal 5102 5230 1.03 + 2 gene_1 test geneid_v1.2 Internal 13675 13737 0.26 + 2 gene_1 test geneid_v1.2 Internal 15525 15806 4.26 + 2 gene_1 test geneid_v1.2 Internal 17034 17318 3.80 + 2 gene_1 test geneid_v1.2 Internal 21599 21618 0.64 + 2 gene_1 test geneid_v1.2 Terminal 23145 23375 0.61 + 0 gene_1 Gene 2 (Forward). 2 exons. 181 aa. Score = 10.263193 test geneid_v1.2 First 74617 74854 6.35 + 0 gene_2 test geneid_v1.2 Terminal 74929 75233 3.91 + 2 gene_2 Gene 3 (Reverse). 5 exons. 197 aa. Score = 7.990742 test geneid_v1.2 Terminal 94916 95043 -0.44 - 2 gene_3 test geneid_v1.2 Internal 95943 96084 1.53 - 0 gene_3 test geneid_v1.2 Internal 96314 96443 2.43 - 1 gene_3 test geneid_v1.2 Internal 97054 97185 4.67 - 1 gene_3 test geneid_v1.2 First 98244 98302 -0.20 - 0 gene_3 Gene 4 (Forward). 15 exons. 766 aa. Score = 46.549015 test geneid_v1.2 First 101952 102061 -1.42 + 0 gene_4 test geneid_v1.2 Internal 102210 102340 -0.15 + 1 gene_4 test geneid_v1.2 Internal 103300 103505 3.34 + 2 gene_4 test geneid_v1.2 Internal 103932 104129 4.76 + 0 gene_4 test geneid_v1.2 Internal 105331 105459 4.56 + 0 gene_4 test geneid_v1.2 Internal 105609 105797 3.81 + 0 gene_4 test geneid_v1.2 Internal 106357 106530 5.45 + 0 gene_4 test geneid_v1.2 Internal 106774 106936 1.28 + 0 gene_4 test geneid_v1.2 Internal 107245 107381 2.61 + 2 gene_4 test geneid_v1.2 Internal 108664 108840 2.52 + 0 gene_4 test geneid_v1.2 Internal 111360 111507 1.14 + 0 gene_4 test geneid_v1.2 Internal 111666 111777 4.83 + 2 gene_4 test geneid_v1.2 Internal 112186 112315 4.80 + 1 gene_4 test geneid_v1.2 Internal 112714 112918 6.00 + 0 gene_4 test geneid_v1.2 Terminal 113402 113490 3.02 + 2 gene_4 Gene 5 (Forward). 15 exons. 1040 aa. Score = 51.141949 test geneid_v1.2 First 116217 116709 1.18 + 0 gene_5 test geneid_v1.2 Internal 116799 116913 4.26 + 2 gene_5 test geneid_v1.2 Internal 117437 117484 0.05 + 1 gene_5 test geneid_v1.2 Internal 118677 118807 3.22 + 1 gene_5 test geneid_v1.2 Internal 119091 119296 7.73 + 2 gene_5 test geneid_v1.2 Internal 121626 121823 6.17 + 0 gene_5 test geneid_v1.2 Internal 121989 122117 2.09 + 0 gene_5 test geneid_v1.2 Internal 123644 123832 2.08 + 0 gene_5 test geneid_v1.2 Internal 124010 124183 7.03 + 0 gene_5 test geneid_v1.2 Internal 124361 124520 3.46 + 0 gene_5 test geneid_v1.2 Internal 132128 132308 2.65 + 2 gene_5 test geneid_v1.2 Internal 137494 137585 1.72 + 1 gene_5 test geneid_v1.2 Internal 139123 139392 4.46 + 2 gene_5 test geneid_v1.2 Internal 139835 140116 3.25 + 2 gene_5 test geneid_v1.2 Terminal 150538 150989 1.80 + 2 gene_5 Gene 6 (Forward). 6 exons. 314 aa. Score = 20.532181 test geneid_v1.2 First 159435 159556 0.89 + 0 gene_6 test geneid_v1.2 Internal 177915 177947 0.49 + 1 gene_6 test geneid_v1.2 Internal 190046 190173 -1.22 + 1 gene_6 test geneid_v1.2 Internal 192477 192743 17.00 + 2 gene_6 test geneid_v1.2 Internal 195269 195550 1.81 + 2 gene_6 test geneid_v1.2 Internal 196514 196624 1.56 + 2 gene_6

% geneid -G test.fasta

2. Introducing sequence homology information

## Homology information: HSP test BLASTN HSP 74000 75500 50.000 - . test BLASTN HSP 76000 76500 100.000 - . test BLASTN HSP 78000 79500 50.000 - .

## date Mon Oct 8 10:21:06 2003 ## source-version: geneid v 1.2 -- geneid@imim.es ## Sequence test - Length = 198285 bps # Optimal Gene Structure. 6 genes. Score = 209.270570 # Gene 1 (Forward). 8 exons. 525 aa. Score = 25.246988 Internal 3698 3982 8.69 + 2 1 5.39 1.69 23.61 0.00 AA 1: 96 gene_1 Internal 4612 4890 5.95 + 2 1 3.01 2.36 19.33 0.00 AA 96:189 gene_1 Internal 5102 5230 1.03 + 2 1 0.20 2.06 11.69 0.00 AA 189:232 gene_1 Internal 13675 13737 0.26 + 2 1 2.23 5.66 1.33 0.00 AA 232:253 gene_1 Internal 15525 15806 4.26 + 2 1 5.61 2.81 11.79 0.00 AA 253:347 gene_1 Internal 17034 17318 3.80 + 2 1 5.76 1.67 12.10 0.00 AA 347:442 gene_1 Internal 21599 21618 0.64 + 2 0 4.61 5.66 -0.07 0.00 AA 442:448 gene_1 Terminal 23145 23375 0.61 + 0 0 5.33 0.00 7.28 0.00 AA 449:525 gene_1

test|geneid_v1.2_predicted_protein_1|525_AA ctPTPMWPDDLQNHTFLHTVYCQDGSPSVGLSEAYDEDQLFFFDFSQNTRVPRLPEFADW AQEQGDAPAILFDKEFCEWMIQQIGPKLDGKIPVSRGFPIAEVFTLKPLEFGKPNTLVCF VSNLFPPMLTVNWQHHSVPVEGFGPTFVSAVDGLSFQAFSYLNFTPEPSDIFSCIVTHEI DRYTAIAYWVPRNALPSDLLENVLCGVAFGLGVLGIIVGIVLIIYFRKPCSGEQSMITFL PLLLGLSLGCTGAGGFVAHVESTCLLDDAGTPKDFTYCISFNKDLLTCWDPEENKMAPCE FGVLNSLANVLSQHLNQKDTLMQRLRNGLQNCATHTQPFWGSLTNRTRPPSVQVAKTTPF NTREPVMLACYVWGFYPAEVTITWRKNGKLVMPHSSAHKTAQPNGDWTYQTLSHLALTPS YGDTYTCVVEHIGAPEPILRDWRKAVPFQADAGSKKKPGSMGAIQCHAGQHLRQTPGAEV LRVGPEGQMEDRKYIHNKKEKRQCCGVEREVQNLGFFWPWTMTSA*

# Gene 2 (Reverse). 11 exons. 537 aa. Score = 51.309784 Terminal 26805 26994 0.68 - 1 0 0.00 0.27 15.05 0.00 AA 474:537 gene_2 Internal 47107 47188 -0.31 - 2 2 4.09 1.96 3.90 0.00 AA 447:474 gene_2 Internal 70660 70831 0.57 - 0 1 2.22 0.79 10.66 0.00 AA 390:447 gene_2 Internal 73992 74191 1.63 - 2 0 2.48 -3.18 2.88 6.40 AA 323:389 gene_2 Internal 74475 74801 11.88 - 2 1 -1.55 0.73 17.45 10.89 AA 214:323 gene_2 Internal 74925 75006 -0.62 - 0 1 -5.56 6.63 3.77 2.73 AA 187:214 gene_2 Internal 76083 76212 18.65 - 1 0 -0.38 -6.11 5.24 25.95 AA 143:186 gene_2 Internal 76337 76368 -0.07 - 0 2 -0.89 -0.67 -0.06 6.39 AA 133:143 gene_2 Internal 76398 76516 18.53 - 2 0 -0.67 2.24 6.31 20.56 AA 93:132 gene_2 Internal 77306 77382 -2.88 - 1 1 4.14 -2.09 3.47 0.00 AA 67: 93 gene_2 First 78038 78237 3.25 - 0 2 2.39 -3.03 6.19 6.66 AA 1: 67 gene_2

test|geneid_v1.2_predicted_protein_2|537_AA MQDLQAKNYVMLVNDIKEDLFSLYLCGEKYCSWIGRFNIVNMSILPKPIYKFNTIPIKIF ARFVNYRRVCGYFLRTQKRENQNQRVHEYMCTVLLLLNHFLHVLEELIGIDGQNKNFNIA ANDRRVSERVPNVKDCMHVCGKEADIGASLTCEKKASFDEKKFSLFLVNTKKCNRNFKGS RPENVTVRGHYPPLHCFLVPEPDTLAPSLQQQLIFVCWTICRQDVHFIPLLGFFAQLLVD TPTGMFGRRHHRGSRRGVVLQDPLEGPLRGRGGRHCRVLRLSAQGRCLAWGPRTEGSALA ETSRQTRSPLKAKAAAPAASEREVQKEVSGRKIAFFTNSELNNGEMEQLGIHRQDNKIKM KLDLSLTPYAKFNSNWIGLLESRSSRPAWECKNKTVVKVLTKLYEGLGKIEKEKTIENSS ILITDITDVRDHRLQSSKGSPTRNRPGKTLGFKNDFLEDNEITEIITGITEDSHRKNIN GAGTIEHSRAIGGEKDNKEEEKEEQQFNLRLIPSAKIDSIWITNFYAKCKTIKLLE

# Gene 3 (Reverse). 7 exons. 298 aa. Score = 14.490652 Terminal 78787 79006 6.99 - 1 0 0.00 3.23 8.30 7.23 AA 225:298 gene_3 Internal 79267 79446 0.97 - 1 2 -3.15 -3.00 10.41 6.00 AA 165:225 gene_3 Internal 87121 87151 -1.90 - 2 2 -0.33 5.16 1.76 0.00 AA 155:165 gene_3 Internal 95943 96084 1.53 - 0 1 1.04 1.08 13.14 0.00 AA 108:155 gene_3 Internal 96314 96443 2.43 - 1 0 5.34 4.11 4.41 0.00 AA 64:107 gene_3 Internal 97054 97185 4.67 - 1 2 0.34 2.74 19.56 0.00 AA 20: 64 gene_3 First 98244 98302 -0.20 - 0 2 3.60 1.52 5.57 0.00 AA 1: 20 gene_3 >test|geneid_v1.2_predicted_protein_3|298_AA MAVEFDGGVVMGSDSRVSAGEAVVNRVFDKLSPLHERIYCALSGSAADAQAVADMAAYQL ELHGIELEEPPLVLAAANVVRNISYKYREDLSAHLMVAGWDQREGGQVYGTLGGMLTRQP FAIGGSGSTFIYGYVDAAYKPGMSPEECRRFTTDVKFLKQKWFRRKYLGTNSFNEEFYQR FKEELTPINLFQKIEAEEAFPSLFYKARITSIPKPNNDNGKKRKLNIGVEEIFLYLIKIV YKNPMVNILDSERLNSFYLKSGTRQECPLSPLLFTVLEVLDSAIGMKKEIKGIQIVK*

Gene 4 (Forward). 15 exons. 766 aa. Score = 46.549015 First 101952 102061 -1.42 + 0 2 1.16 0.34 6.71 0.00 AA 1: 37 gene_4 Internal 102210 102340 -0.15 + 1 1 4.04 -1.92 8.94 0.00 AA 37: 81 gene_4 Internal 103300 103505 3.34 + 2 0 4.52 4.14 7.86 0.00 AA 81:149 gene_4 Internal 103932 104129 4.76 + 0 0 3.85 -0.04 18.67 0.00 AA 150:215 gene_4 Internal 105331 105459 4.56 + 0 0 5.35 3.92 10.00 0.00 AA 216:258 gene_4 Internal 105609 105797 3.81 + 0 0 5.64 0.78 12.40 0.00 AA 259:321 gene_4 Internal 106357 106530 5.45 + 0 0 3.90 3.52 15.00 0.00 AA 322:379 gene_4 Internal 106774 106936 1.28 + 0 1 3.56 0.52 9.56 0.00 AA 380:434 gene_4 Internal 107245 107381 2.61 + 2 0 3.85 4.71 6.19 0.00 AA 434:479 gene_4 Internal 108664 108840 2.52 + 0 0 4.41 -1.36 14.21 0.00 AA 480:538 gene_4 Internal 111360 111507 1.14 + 0 1 4.01 0.44 8.68 0.00 AA 539:588 gene_4 Internal 111666 111777 4.83 + 2 2 4.40 5.44 9.82 0.00 AA 588:625 gene_4 Internal 112186 112315 4.80 + 1 0 3.55 3.50 13.92 0.00 AA 625:668 gene_4 Internal 112714 112918 6.00 + 0 1 2.72 1.65 20.97 0.00 AA 669:737 gene_4 Terminal 113402 113490 3.02 + 2 0 5.19 0.00 12.26 0.00 AA 737:766 gene_4

test|geneid_v1.2_predicted_protein_4|766_AA MAIPFFTGRLTDWILQDGSADTFTRNLTLMSILTIASAVLEFVGDGIYNNTMGHVHSHLQ GEVFGAVLRQETEFFQQNQTGNIMSRVTEDTSTLSDSLSENLSLFLWYLVRGLCLLGIML WGSVSLTMVTLITLPLLFLLPKKVGKWYQLLEVQVRESLAKSSQVAIEALSAMPTVRSFA NEEGEAQKFREKLQEIKTLNQKEAVAYAVNSWTTSISGMLLKVGILYIGGQLVTSGAVSS GNLVTFVLYQMQFTQAVEVLLSIYPRVQKAVGSSEKIFEYLDRTPRCPPSGLLTPLHLEG LVQFQDVSFAYPNRPDVLVLQGLTFTLRPGEVTALVGPNGSGKSTVAALLQNLYQPTGGQ LLLDGKPLPQYEHRYLHRQVAAVGQEPQVFGRSLQENIAYGLTQKPTMEEITAAAVKSGA HSFISGLPQGYDTEVDEAGSQLSGGQRQAVALARALIRKPCVLILDDATSALDANSQLQV EQLLYESPERYSRSVLLITQHLSLVEQADHILFLEGGAIREGGTHQQLMEKKGCYWAMPT EFFQSLGGDGERNVQIEMAHGTTTLAFKFQHGVIAAVDSRASAGSYISALRVNKVIEINP YLLGTMSGCAADCQYWERLLAKECRLYYLRNGERISVSAASKLLSNMMCQYRGMGLSMGS MICGWDKKGPGLYYVDEHGTRLSGNMFSTGSGNTYAYGVMDSGYRPNLSPEEAYDLGRRA IAYATHRDSYSGGVVNMYHMKEDGWVKVESTDVSDLLHQYREANQ*

Gene 5 (Forward). 15 exons. 1040 aa. Score = 51.141949 First 116217 116709 1.18 + 0 1 4.46 2.44 5.09 0.00 AA 1:165 gene_5 Internal 116799 116913 4.26 + 2 2 5.85 4.63 7.42 0.00 AA 165:203 gene_5 Internal 117437 117484 0.05 + 1 2 6.31 3.70 -1.13 0.00 AA 203:219 gene_5 Internal 118677 118807 3.22 + 1 1 5.18 3.05 8.20 0.00 AA 219:263 gene_5 Internal 119091 119296 7.73 + 2 0 5.08 4.49 17.47 0.00 AA 263:331 gene_5 Internal 121626 121823 6.17 + 0 0 4.30 3.64 17.26 0.00 AA 332:397 gene_5 Internal 121989 122117 2.09 + 0 0 7.47 4.49 1.03 0.00 AA 398:440 gene_5 Internal 123644 123832 2.08 + 0 0 4.08 0.30 11.14 0.00 AA 441:503 gene_5 Internal 124010 124183 7.03 + 0 0 5.53 3.68 16.25 0.00 AA 504:561 gene_5 Internal 124361 124520 3.46 + 0 1 4.54 1.41 12.22 0.00 AA 562:615 gene_5 Internal 132128 132308 2.65 + 2 2 6.44 3.78 5.05 0.00 AA 615:675 gene_5 Internal 137494 137585 1.72 + 1 1 5.36 5.38 1.95 0.00 AA 675:706 gene_5 Internal 139123 139392 4.46 + 2 1 2.30 4.31 14.99 0.00 AA 706:796 gene_5 Internal 139835 140116 3.25 + 2 1 5.08 -0.18 13.27 0.00 AA 796:890 gene_5 Terminal 150538 150989 1.80 + 2 0 1.12 0.00 16.56 0.00 AA 890:1040 gene_5

test|geneid_v1.2_predicted_protein_5|1040_AA MRLPDLRPWTSLLLVDAALLWLLQGPLGTLLPQGLPGLWLEGTLRLGGLWGLLKLRGLLG FVGTLLLPLCLATPLTVSLRALVAGASRAPPARVASAPWSWLLVGYGAAGLSWSLWAVLS PPGAQEKEQDQVNNKVLMWRLLKLSRPDLPLLVAAFFFLVLAVLGETLIPHYSGRVIDIL GGDFDPHAFASAIFFMCLFSFGRHTQTNKLFDKAGTGMSSLSAGCRGGCFTYTMSRINLR IREQLFSSLLRQDLGFFQETKTGELNSRLSSDTTLMSNWLPLNANVLLRSLVKVVGLYGF MLSISPRLTLLSLLHMPFTIAAEKVYNTRHQEVLREIQDAVARAGQVVREAVGGLQTVRS FGAEEHEVCRYKEALEQCRQLYWRRDLERALYLLVRRVLHLGVQMLMLSCGLQQMQDGEL TQGSLLSFMIYQESVGSYVQTLVYIYGDMLSNVGAAEKVFSYMDRQPNLPSPGTLAPTTL QGVVKFQDVSFAYPNRPDRPVLKGLTFTLRPGEVTALVGPNGSGKSTVAALLQNLYQPTG GQVLLDEKPISQYEHCYLHSQVVSVGQEPVLFSGSVRNNIAYGLQSCEDDKVMAAAQAAH ADDFIQEMEHGIYTENPLEVHDILNFSGYFLGIMSSNERICGTKHHQHLFFQDEVMDKTI TGKLRQIVHVKQYFGMGSGWVPWVVALLVNLTRLDSSMTQGTDSPEDFVIQAKADCYFTN GTEKVQFVVRFIFNLEEYVRFDSDVGMFVALTKLGQPDAEQWNSRLDLLERSRQAVDGVC RHNYRLGAPFTVGRKVQPEVTVYPERTPLLHQHNLLHCSVTGFYPGDIKIKWFLNGQEER AGVMSTGPIRNGDWTFQTVVMLEMTPELGHVYTCLVDHSSLLSPVSVEWNAEKSSDKIQH SFMLKTLDKLVIEGTYVKIVRAIYDKPAANIILNGQNLEAFPLKTGRRQECPLSLLLFNI VLEVLARAIRQEKRIKSSQIGKEEVKVFLFADDMIIYLENPIVSAQKLLKLINNFSKVSG YKINVQKLLIFLYTNNSQA*

Gene 6 (Forward). 6 exons. 314 aa. Score = 20.532181 First 159435 159556 0.89 + 0 2 1.25 6.11 4.94 0.00 AA 1: 41 gene_6 Internal 177915 177947 0.49 + 1 2 5.67 4.44 -0.19 0.00 AA 41: 52 gene_6 Internal 190046 190173 -1.22 + 1 1 2.30 0.25 6.88 0.00 AA 52: 95 gene_6 Internal 192477 192743 17.00 + 2 1 4.16 4.31 42.30 0.00 AA 95:184 gene_6 Internal 195269 195550 1.81 + 2 1 3.07 1.41 11.56 0.00 AA 184:278 gene_6 Internal 196514 196624 1.56 + 2 1 2.68 4.53 5.59 0.00 AA 278:314 gene_6

test|geneid_v1.2_predicted_protein_6|314_AA MRDKSSAWPHHQQSCYYNEDEGTEKRGRDGIHQTTVLIHTRDSMTFIHLVPRCTCFMVQG GFKQLKNLQEKSQQILSLEEHECNTFLHNKESLAKDFLVQFKGMCYFTNGTERVRGVARY IYNREEYGRFDSDVGEFQAVTELGRSIEDWNNYKDFLEQERAAVDKVCRHNYEAELRTTL QRQVEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETAGVVSTSLIRNG DWTFQILVMLEITPQRGDIYTCQVEHPSLQSPITVEWRAQSESAQSKMLSGIGGFVLGLI FLGLGLIIRHRGQKag

% geneid -GS sr.gff test.fasta

Multi-fasta files

geneid can process files containing more than one FASTA sequence. Moreover, external information as annotations and HSPs can be provided for every sequence. Requirement: records belonging to the same Locus must be sorted by first position.

Click over every example to see the corresponding output:

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Running Geneid

FASTA format

General considerations

Geneid command line options

Geneid output formats

- Geneid Format

- Gff output format

- XML output format

- Geneid extended output format

Samples

- Prediction of acceptor splice sites

- Prediction of exons

- Gene Prediction

- Geneid samples re annotation

- Geneid samples homology information

Multi-fasta files

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