1. Untar the downloaded file "FragGeneScan_HPC.tar.gz". This will automatically generate the directory "FragGeneScan_HPC".
make clean
make fgs
./run_FragGeneScan.pl -genome=[seq_file_name] -out=[output_file_name] -complete=[1 or 0] -train=[train_file_name] -processes=[processes]
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[seq_file_name]: sequence file name including the full path
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[output_file_name]: output file name including the full path
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[whole_genome]: 1 if the sequence file has complete genomic sequences 0 if the sequence file has short sequence reads
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[train_file_name]: file name that contains model parameters; this file should be 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_5] for Illumina sequencing reads with about 0.5% error rate [illumina_10] for Illumina sequencing reads with about 1% error rateNote that files containing model parameters already exist in the "train" directory.
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[processes]: number of processes used in FragGeneScan. Default 1.
./run_FragGeneScan.pl -genome=./example/NC_000913.fna -out=./example/NC_000913-fgs -complete=1 -train=complete
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[NC_000913.fna]: this sequence file has the complete genomic sequence of E.coli
(NCBI gene predictions for this genome are available under the same folder example/)
./run_FragGeneScan.pl -genome=./example/NC_000913-454.fna -out=./example/NC_000913-454-fgs -complete=0 -train=454_10
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[NC_000913-454.fna]: this sequence file has simulated reads (pyrosequencing, average length = 400 bp and sequencing error = 1%) generated using Metasim
For illumina reads, please use illumina_5 or illumina_10 as the train model.
./run_FragGeneScan.pl -genome=./example/contigs.fna -out=./example/contigs-fgs -complete=1 -train=complete
Note: -complete=1 & -train=complete are used as the parameters.
./run_FragGeneScan.pl -genome=./example/NC_000913.fna -out=./example/NC_000913-fgs -complete=1 -train=complete
1. The first file is "[output_file_name].out", which lists the coordinates of putative genes. This file consists of five columns (start position, end position, strand, frame, score). For example,
>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
2. The second file is "[output_file_name].ffn", which lists nucleotide 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=-
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
4. The fourth file is "[output_file_name].gff" which show the gene prediction results in gff format.
Copyright (C) 2010 Mina Rho, Yuzhen Ye and Haixu Tang.
Copyright (C) 2020 Bruno Cabado.
The source for FragGeneScan_HPC is released under the GNU General Public License as published by the Free Software Foundation, either version 3 of the License (See COPYING.txt).