MetaGene: prokaryotic gene finding from environmental genome shotgun sequences

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ID: 299709
2006
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Abstract
Exhaustive gene identification is a fundamental goal in all metagenomics projects.However, most metagenomic sequences are unassembled anonymous fragments, and conventional gene-finding methods cannot be applied.We have developed a prokaryotic gene-finding program, MetaGene, which utilizes di-codon frequencies estimated by the GC content of a given sequence with other various measures.MetaGene can predict a whole range of prokaryotic genes based on the anonymous genomic sequences of a few hundred bases, with a sensitivity of 95% and a specificity of 90% for artificial shotgun sequences (700 bp fragments from 12 species).MetaGene has two sets of codon frequency interpolations, one for bacteria and one for archaea, and automatically selects the proper set for a given sequence using the domain classification method we propose.The domain classification works properly, correctly assigning domain information to more than 90% of the artificial shotgun sequences.Applied to the Sargasso Sea dataset, MetaGene predicted almost all of the annotated genes and a notable number of novel genes.MetaGene can be applied to wide variety of metagenomic projects and expands the utility of metagenomics.
Reference Key
openalex_W2156701707 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Hideki Noguchi, Jung‐Ho Park, Toshihisa Takagi
Journal Nucleic Acids Research
Year 2006
DOI
10.1093/nar/gkl723
URL
https://doi.org/10.1093/nar/gkl723
Keywords Keywords not found

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