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FragGeneScan | Predicting genes in short and error-prone reads

A gene prediction method which combines sequencing error models and codon usages in a hidden Markov model to improve the prediction of protein-coding region in short reads. The performance of FragGeneScan was comparable to Glimmer and MetaGene for complete genomes. But for short reads, FragGeneScan consistently outperformed MetaGene (accuracy improved ∼62% for reads of 400 bases with 1% sequencing errors, and ∼18% for short reads of 100 bases that are error free). When applied to metagenomes, FragGeneScan recovered substantially more genes than MetaGene predicted (>90% of the genes identified by homology search), and many novel genes with no homologs in current protein sequence database.

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FragGeneScan forum

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FragGeneScan classification

FragGeneScan specifications

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

FragGeneScan distribution

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FragGeneScan support

Documentation

Maintainer

  • Yuzhen Ye <>

Credits

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Publications

Institution(s)

School of Informatics and Computing, Indiana University, Bloomington, IN; Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, USA

Funding source(s)

National Institutes of Health (1R01HG004908-02); National Science Foundation (CAREER award DBI-0845685)

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