articleNucleic Acids ResearchOct 5, 2006GOLD OA

MetaGene: prokaryotic gene finding from environmental genome shotgun sequences

HNHideki NoguchiJPJung‐Ho ParkTTToshihisa Takagi

The University of Tokyo

PubMed
Indexed incrossrefdoajpubmed

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…

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Topics & keywords

Topics
Keywords
  • Biology
  • Metagenomics
  • Shotgun
  • Computational biology
  • Gene
  • Shotgun sequencing
  • Genome
  • Genetics
UN Sustainable Development Goals
  • Life below water
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