Note to the users: the latest release is significantly improved in terms of performance. For large files of assembly contigs, the running time could be reduced from days to a few mins. (Read more about this in the “releases” file included in the package).

Description

FragGeneScan is an application for finding (fragmented) genes in short reads. It can also be applied to predict prokaryotic genes in incomplete assemblies or complete genomes.

FragGeneScan was first released through omics website (http://omics.informatics.indiana.edu/FragGeneScan/) in March 2010, where you can find its old releases.

FragGeneScan migrated to SourceForge in October, 2013. (https://sourceforge.net/projects/fraggenescan/)

FragGeneScan migrated to Github for easier maintenance in March, 2017. (https://github.com/COL-IU/FragGeneScan.git)

Installation

To install FragGeneScan, please follow the steps below:

1. Clone the repository: git clone https://github.com/COL-IU/FragGeneScan.git

2. Make sure that you also have a C compiler such as “gcc” and perl interpreter.

3. Run “makefile” to compile and build excutable “FragGeneScan” make clean make fgs

Running the program

1. To run FragGeneScan,

./run_FragGeneScan.pl -genome=[seq_file_name] -out=[output_file_name] -complete=[1 or 0] -train=[train_file_name] -thread=[num_thread]

[seq_file_name]: sequence file name including the full path [output_file_name]: output file name including the full path [whole_genome]: 1 if the sequence file has complete genomic sequences 0 if the sequence file has short sequence reads [train_file_name]: //NSCCN/fraggenescan/tree/master/filenamethatcontainsmodelparameters;thisfileshouldbeinthe”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_5] for Illumina sequencing reads with about 0.5% error rate [illumina_10] for Illumina sequencing reads with about 1% error rate [num_thread]: number of thread used in FragGeneScan. Default 1.

2. To test FragGeneScan with a complete genomic sequence,

./run_FragGeneScan.pl -genome=./example/NC_000913.fna -out=./example/NC_000913-fgs -complete=1 -train=complete

3. To test FragGeneScan with sequencing reads,

./run_FragGeneScan.pl -genome=./example/NC_000913-454.fna -out=./example/NC_000913-454-fgs -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

For illumina reads, please use illumina_5 or illumina_10 as the train model.

4. To test FragGeneScan with assembly contigs, ./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.

Output

Upon completion, FragGeneScan generates four files.

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. [output_file_name].gff gene prediction results in gff format.

Citation

If you use FragGeneScan, please cite: Mina Rho, Haixu Tang, and Yuzhen Ye. FragGeneScan: Predicting Genes in Short and Error-prone Reads. Nucl. Acids Res., 2010 doi: 10.1093/nar/gkq747

License

Copyright (C) 2010 Mina Rho, Yuzhen Ye and Haixu Tang. You may redistribute this software under the terms of the GNU General Public License.