FragGeneScan protocols

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FragGeneScan specifications

Information


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 No

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Publication for FragGeneScan

FragGeneScan in pipelines

 (19)
2018
PMCID: 5749766
PMID: 29293601
DOI: 10.1371/journal.pone.0190266

[…] metagenome reads were filtered and assembled by using megahit [] with default k-mer options. subsequently, all contigs over 1,000 bp were used to identify the proteins in the microbiome by using fraggenescan []. the predicted proteins in each sample were clustered with the proteins in 13 complete reference synechococcus. in order to analyze the various aspects, cd-hit [] clustering […]

2017
PMCID: 5348496
PMID: 28352255
DOI: 10.3389/fmicb.2017.00391

[…] was carried out using velvet v.1.2.10 (), by setting 61 as k-mer length, 200 as insert length, and 300 as minimum contig length. open reading frames were found from both reads and contigs using fraggenescan v.1.19, with the training for illumina sequencing reads with about 0.5% error rate (). the second database was a selection of all bacterial, archaeal, fungal and gut microbiota sequences […]

2017
PMCID: 5461723
PMID: 28587624
DOI: 10.1186/s12864-017-3828-x

[…] made in cytoscape., for the cases where genome organization of certain gene complexes were compared between different species (i.e., fox and dsr genes), we performed a de novo orf prediction using fraggenescan [] to get the genome positions, gene orientations and gene sizes. all predicted peptides were then compared by blastp to a reference database with the genes of interest and then hits […]

2017
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 metawatt. orfs were detected using fraggenescan, and protein homologs were identified through blastp searches against the seed database (www.theseed.org). only hits to reference proteins with at least 60% amino acid similarity […]

2017
PMCID: 5570362
PMID: 28837661
DOI: 10.1371/journal.pone.0181753

[…] removed using ribopicker v.0.4.3 []. contigs were assembled de novo using clc assembly cell (version 3. 22.55708) []. putative open reading frames on the assembled contigs were called using fraggenescan []. predicted protein sequences were annotated by hidden markov models for pfam and tigrfam, and by blastp against phylodb 1.06 with an e-value threshold of 1e-3. phylodb […]


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FragGeneScan in publications

 (98)
PMCID: 5943556
PMID: 29774016
DOI: 10.3389/fmicb.2018.00869

[…] (boisvert et al., ) assembler. secondly, to explore contig features and gene contents, contigs were submitted to the mg-rast webserver (glass et al., ) and orf prediction was conducted using the fraggenescan tool (rho et al., ). afterwards, contigs were annotated with the blat tool implemented in mg-rast against the seed database using stringent filtering parameters (1e−12 as p-value, 85% […]

PMCID: 5938574
PMID: 29618526
DOI: 10.1098/rsif.2017.0387

[…] classification or functional annotation from sequence data where there is ample data for training. neural networks have been applied successfully to gene annotation (e.g. orphelia [] and fraggenescan []). representations (similar to word2vec [] in nlp) for protein family classification have been introduced and classified with a skip-gram neural network []. rnns show good performance […]

PMCID: 5855605
PMID: 29382070
DOI: 10.3390/ijms19020383

[…] have been optimized to use unassembled reads for functional prediction. briefly, a functional analysis is based on genes prediction to infer their probable functions. different methods, such as fraggenescan [], metagenemark [], and glimmer-mg [], have been developed and optimized for this aim. once the genes have been identified, specific databases can be used for functional predictions, […]

PMCID: 5787071
PMID: 29410661
DOI: 10.3389/fmicb.2018.00043

[…] of 70% identity to ribosomal sequences were identified () and sequences were clustered at 97% identity (). after removal of rrna sequences, putative protein coding features were predicted using fraggenescan () and clustered at 90% identity. protein similarity search against the m5nr protein database was done with blat (). for post-processing taxonomic and functional analysis, the kegg (; ) […]

PMCID: 5758534
PMID: 29354108
DOI: 10.3389/fmicb.2017.02622

[…] were further restricted at 45 and 65% for family- and genus-level taxonomic groups, respectively (konstantinidis et al., )., to provide functional profiles of metagenomes and metatranscriptomes, fraggenescan (rho et al., ) based on the hidden markov model was used to predict open reading frames (orfs) on putative mrna reads. the orfs were queried to identify conserved protein families […]


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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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