FragGeneScan pipeline

FragGeneScan specifications


Unique identifier OMICS_01484
Name FragGeneScan
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C, Perl
Computer skills Advanced
Stability Stable
Maintained Yes



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  • person_outline Yuzhen Ye <>

Publication for FragGeneScan

FragGeneScan IN pipelines

PMCID: 5519670
PMID: 28729646
DOI: 10.1038/s41598-017-05590-9

[…] a minimum of 5x coverage were first separated into bacterial and archaeal bins via interpolated markov modeling, tetranucleotide binning, and blast performed in metawatt47. orfs were detected using fraggenescan48, and protein homologs were identified through blastp searches against the seed database ( only hits to reference proteins with at least 60% amino acid similarity […]

PMCID: 5591210
PMID: 28887527
DOI: 10.1038/s41598-017-11385-9

[…] with default options (supplementary table s5). the shotgun metagenome reads were assembled by using megahit30 with default k-mer options. subsequently, genes were predicted from the contigs by using fraggenescan31. the genes longer than 500 bps were retained and clustered with the bacillus core genes by using cd-hit23. two different similarity thresholds of 70% and 90% were applied to compare […]

PMCID: 5649170
PMID: 28731472
DOI: 10.1038/ismej.2017.114

[…] and vectordb to remove artifacts and ribosomal rna sequences. reads were assembled into transcript contigs using clc genomics workbench (v. 6) (qiagen, germantown, md, usa), orfs were called with fraggenescan, and the reads were then mapped back to the assembled transcript orfs using clc. orfs were annotated by blastp vs phylodb and hmmscan with pfam/tigrfam (asplund-samuelsson et al., 2016). […]

PMCID: 4958695
PMID: 27324572
DOI: 10.1016/j.syapm.2016.05.006

[…] from further analysis. cable bacterial 16s rrna genes were extracted from the assemblies as described previously [36]. open reading frames (orfs) were predicted on the extracted contigs using fraggenescan version 1.19 [34]. orfs coding for dsra and dsrb were identified and extracted using megan version 4.70.4 [13] based on blastp hits to ncbi's nr database (january 25th, 2015 version). […]

PMCID: 4226467
PMID: 25383623
DOI: 10.1371/journal.pone.0110505

[…] of processed sequence reads using metavelvet resulted in 142,061 contigs with a mean n50 = 715 bp (±337.32; sd) per sample. approximately 175,375 orfs were predicted from these contigs using fraggenescan. the orfs were annotated against the pfam database;. the mean number of pfam protein families identified in the ovine rumen microbiome at the basal control level was 2,765±57 (table s1). […]

FragGeneScan institution(s)
School of Informatics and Computing, Indiana University, Bloomington, IN; Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, USA
FragGeneScan funding source(s)
National Institutes of Health (1R01HG004908-02); National Science Foundation (CAREER award DBI-0845685)

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