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Running Geneid
Running geneid
Table of contents:
- FASTA format
- General considerations
- Geneid command line options
- Geneid output formats
- Samples
- Multi-fasta files
- INDEX
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.
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
Selection of genomic elements to display
|
- Geneid format (default)
- Gff output format
- Xml output format
- Geneid extended output format
- Back to top
Click over every available format to see a detailed description:
- Score for both signals defining exon
- Protein coding potential (exon content)
- Homology information score (blast HSPs): provided by user
Gene extracted from human Chromosome 22 predictions (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:
|
AA | Amino acids corresponding to the exon translation |
Key | Gene identifier |
Gene extracted from a human prediction (gff 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 |
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 |
- Score for both signals defining exon
- Protein coding potential (exon content)
- Homology information score (SR regions): provided by user
Gene extracted from a human prediction (geneid eXtended 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:
|
AA | Amino acids corresponding to the exon translation |
Key | Gene identifier |
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
- Back to top
diff - This the sequence used to generate these outputs:
test.fa
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
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 |
geneid samples: exons
geneid samples: exons | ||||||
2. gff format
|
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 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
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
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
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
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
|
% bin/geneid -vP param/human3iso.param test.fa |
2. gff format
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 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
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
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
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
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
|
% bin/geneid -XP param/human3iso.param test.fa |
4. eXtended format (gff)
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 | |||||||||
2. Introducing evidences (without group)
3. Introducing evidences (with group)
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geneid samples: homology information
geneid samples: homology information | ||||||
2. Introducing sequence homology information
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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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Enrique Blanco Garcia © 2003