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 <>

FragGeneScan article

FragGeneScan citations

PMCID: 4958695

[…] 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: 4679923

[…] was conducted by selecting the best blastx score result between the three blasts run for each contig., contigs matching with amoeba-infecting giant viruses were extracted and translated using the fraggenescan tool (rho et al., 2010), according to the “short” and “complete” parameters. predicted open reading frames (orf) were then compared to the megavirales database using the blastp program […]

PMCID: 4426941

[…] such as qiime111 (see section on marker gene metagenomics) for the efficient taxonomic assignment of these sequences. for functional analysis and annotation of cds sequences, ebi metagenomics uses fraggenescan to obtain protein coding sequences and thereafter utilizes databases such as interpro, which is a composite, cumulative system comprised of multiple databases of protein families, […]

PMCID: 4226467

[…] 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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