FragGeneScan: predicting genes in short and error-prone reads

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ID: 303713
2010
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Abstract
The advances of next-generation sequencing technology have facilitated metagenomics research that attempts to determine directly the whole collection of genetic material within an environmental sample (i.e. the metagenome). Identification of genes directly from short reads has become an important yet challenging problem in annotating metagenomes, since the assembly of metagenomes is often not available. Gene predictors developed for whole genomes (e.g. Glimmer) and recently developed for metagenomic sequences (e.g. MetaGene) show a significant decrease in performance as the sequencing error rates increase, or as reads get shorter. We have developed a novel gene prediction method FragGeneScan, 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.
Reference Key
openalex_W2069689025 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Mina Rho, Haixu Tang, Yuzhen Ye
Journal Nucleic Acids Research
Year 2010
DOI
10.1093/nar/gkq747
URL
https://academic.oup.com/nar/article-pdf/38/20/e191/16772703/gkq747.pdf
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