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README
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Installation
=============
To install FragGeneScanPlus, please follow the steps below:
1. Untar the downloaded file "FragGeneScanPlus.tar.gz". This will automatically generate the directory "FragGeneScan".
2. Make sure that you also have the gcc C compiler.
3. Run "makefile" to compile and build executable "FGS+"
make clean
make
Running the program
====================
1. To run FragGeneScanPlus,
USAGE: ./FGS+ -s [seq_file_name] -m [max_mem_use] -o [output_file_name] -w [1 or 0] -t [train_file_name] -p [thread_num] -e [1 or 0] -d [1 or 0]
EXAMPLE USAGE: ./FGS+ -s example/NC_000913-454.fna -o output -w 0 -t 454_5 -p 16
MINIMAL USAGE: ./FGS+ -s [seq_file_name] -o [output_file_name] -w [1 or 0] -t [train_file_name]
INFO: FragGeneScanPlus will only output the amino acid files by default. To obtain the gene coordinate information set -e to 1 and for the DNA files set -d to 1
Mandatory parameters
-s [seq_file_name]: sequence file name including the full path
-o [output_file_name]: output file name including the full path
-w [1 or 0]: 1 if the sequence file has complete genomic sequences
0 if the sequence file has short sequence reads
-t [train_file_name]: file name that contains model parameters; this file should be in the "train" directory
Note that four files containing model parameters already exist in the "train" directory
[complete] for complete genomic sequences or short sequence reads without sequencing error
[sanger_5] for Sanger sequencing reads with about 0.5% error rate
[sanger_10] for Sanger sequencing reads with about 1% error rate
[454_5] for 454 pyrosequencing reads with about 0.5% error rate
[454_10] for 454 pyrosequencing reads with about 1% error rate
[454_30] for 454 pyrosequencing reads with about 3% error rate
[illumina_1] for Illumina sequencing reads with about 0.1% error rate
[illumina_5] for Illumina sequencing reads with about 0.5% error rate
[illumina_10] for Illumina sequencing reads with about 1% error rate
Optional flags
-p [thread_num] The number of threads used by FragGeneScan; default is 1 thread.
-e [1 or 0] Output metadata for sequences.
-d [1 or 0] Output DNA file.
-m [max_mem_usage] Maximum amount of memory to be used per thread, in megabytes, default 1024 for 1GB
2. To test FragGeneScanPlus with a complete genomic sequence,
./FGS+ -genome=./example/NC_000913.fna -out=./example/NC_000913.test -complete=1 -train=complete
[NC_000913.fna]: this sequence file has the complete genomic sequence of E.coli
3. To test FragGeneScanPlus with sequencing reads,
./FGS+ -genome=./example/NC_000913-454.fna -out=./example/NC_000913-454.test -complete=0 -train=454_10
[NC_000913-454.fna]: this sequence file has simulated reads (pyrosequencing, average length = 400 bp and sequencing error = 1%) generated using Metasim
Output
============
Upon completion, FragGeneScanPlus can generate three files [output_file_name].faa , [output_file_name].out and [output_file_name].ffn.
1. The "[output_file_name].faa" file lists amino acid sequences corresponding to the putative genes in "[output_file_name].out".
The "[output_file_name].faa" file is always generated and needs no flags to trigger it's output.
An example of the "[output_file_name].faa" file looks like this,
>gi|49175990|ref|NC_000913.2| Escherichia coli str. K-12 substr. MG1655, complete genome start=108 e
nd=338 strand=-
VVTSLPLVEKKSPHCQVRAFFCVSCTRQPAPLPVVMVMVVVMVVLMRFMDVVYSVIFICLCAMPILVKVFSDLSQ
>gi|49175990|ref|NC_000913.2| Escherichia coli str. K-12 substr. MG1655, complete genome start=343 e
nd=2799 strand=+
LKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKH
VLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLG
RNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDE
LPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVG
DGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGV
ANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKF
LYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEP
VLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTA
AGVFADLLRTLSWKLGV
>gi|49175990|ref|NC_000913.2| Escherichia coli str. K-12 substr. MG1655, complete genome start=2801
end=3733 strand=+
VKVYAPASSANMSVGFDVLGAAVTPVDGALLGDVVTVEAAETFSLNNLGRFADKLPSEPRENIVYQCWERFCQELGKQIPVAMTLEKNMPIGSGLGSSAC
SVVAALMAMNEHCGKPLNDTRLLALMGELEGRISGSIHYDNVAPCFLGGMQLMIEENDIISQQVPGFDEWLWVLAYPGIKVSTAEARAILPAQYRRQDCI
AHGRHLAGFIHACYSRQPELAAKLMKDVIAEPYRERLLPGFRQARQAVAEIGAVASGISGSGPTLFALCDKPETAQRVADWLGKNYLQNQEGFVHICRLD
TAGARVLEN
2. The "[output_file_name].out" file lists the coordinates of putative genes. This file consists of five columns (start position, end position, strand, frame, score).
This file is not automatically generated. To obtain this file set the -e flag to 1
An example of the "[output_file_name].out" file looks like this,
>gi|49175990|ref|NC_000913.2| Escherichia coli str. K-12 substr. MG1655, complete genome
108 440 - 3 1.378688
337 2799 + 1 1.303498
2801 3733 + 2 1.317386
3734 5020 + 2 1.293573
5234 5530 + 2 1.354725
5683 6459 - 1 1.290816
6529 7959 - 1 1.326412
8238 9191 + 3 1.286832
9306 9893 + 3 1.317067
3. The "[output_file_name].ffn" file lists nucleotide sequences corresponding to the putative genes in "[output_file_name].out".
This file is not automatically generated. To obtain this file set the -d flag to 1
An example of the "[output_file_name].out" file looks like this,
>gi|49175990|ref|NC_000913.2| Escherichia coli str. K-12 substr. MG1655, complete genome start=108 e
nd=338 strand=-
GTTGTTACCTCGTTACCTTTGGTCGAAAAAAAAAGCCCGCACTGTCAGGTGCGGGCTTTTTTCTGTGTTTCCTGTACGCGTCAGCCCGCACCGTTACCTG
TGGTAATGGTGATGGTGGTGGTAATGGTGGTGCTAATGCGTTTCATGGATGTTGTGTACTCTGTAATTTTTATCTGTCTGTGCGCTATGCCTATATTGGT
TAAAGTATTTAGTGACCTAAGTCAA
>gi|49175990|ref|NC_000913.2| Escherichia coli str. K-12 substr. MG1655, complete genome start=343 e
nd=2799 strand=+
TTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCC
TCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTAT
TTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACAT
GTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCG
3. The third file is '[output_file_name].faa", which lists amino acid sequences corresponding to the putative genes in "[output_file_name].out". For example,
>gi|49175990|ref|NC_000913.2| Escherichia coli str. K-12 substr. MG1655, complete genome start=108 e
nd=338 strand=-
VVTSLPLVEKKSPHCQVRAFFCVSCTRQPAPLPVVMVMVVVMVVLMRFMDVVYSVIFICLCAMPILVKVFSDLSQ
>gi|49175990|ref|NC_000913.2| Escherichia coli str. K-12 substr. MG1655, complete genome start=343 e
nd=2799 strand=+
LKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKH
VLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLG
RNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDE
LPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVG
DGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGV
ANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKF
LYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEP
VLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTA
AGVFADLLRTLSWKLGV
>gi|49175990|ref|NC_000913.2| Escherichia coli str. K-12 substr. MG1655, complete genome start=2801
end=3733 strand=+
VKVYAPASSANMSVGFDVLGAAVTPVDGALLGDVVTVEAAETFSLNNLGRFADKLPSEPRENIVYQCWERFCQELGKQIPVAMTLEKNMPIGSGLGSSAC
SVVAALMAMNEHCGKPLNDTRLLALMGELEGRISGSIHYDNVAPCFLGGMQLMIEENDIISQQVPGFDEWLWVLAYPGIKVSTAEARAILPAQYRRQDCI
AHGRHLAGFIHACYSRQPELAAKLMKDVIAEPYRERLLPGFRQARQAVAEIGAVASGISGSGPTLFALCDKPETAQRVADWLGKNYLQNQEGFVHICRLD
TAGARVLEN