Home LiteratureArticle Details
PMID: 17028096 Published · ppublish English Evaluation Study Journal Article Research Support, Non-U.S. Gov't

MetaGene: prokaryotic gene finding from environmental genome shotgun sequences.

Nucleic acids research ·Vol. 34 ·No. 19 ·2006-00-00 ·Pages 5623-30

Noguchi H, Park J, Takagi T

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.

MeSH Terms
Computational Biology Environment GC Rich Sequence Genes, Archaeal Genes, Bacterial Genome, Archaeal Genome, Bacterial Genomics/methods Internet Oceans and Seas Open Reading Frames Software
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Noguchi Hideki
Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277-8562, Japan. hide@cb.k.u-tokyo.ac.jp
Park Jungho
Takagi Toshihisa
References (30)
30 references, click to expand
  1. Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes.
    Trends Microbiol. 2001 Jul;9(7):335-43 PMID: 11435108
  2. How to interpret an anonymous bacterial genome: machine learning approach to gene identification.
    Genome Res. 1998 Nov;8(11):1154-71 PMID: 9847079
  3. On the convergence of a clustering algorithm for protein-coding regions in microbial genomes.
    Bioinformatics. 2000 Apr;16(4):367-71 PMID: 10869034
  4. Bioinformatics for whole-genome shotgun sequencing of microbial communities.
    PLoS Comput Biol. 2005 Jul;1(2):106-12 PMID: 16110337
  5. Exploring prokaryotic diversity in the genomic era.
    Genome Biol. 2002;3(2):REVIEWS0003 PMID: 11864374
  6. A hidden Markov model that finds genes in E. coli DNA.
    Nucleic Acids Res. 1994 Nov 11;22(22):4768-78 PMID: 7984429
  7. Microbial gene identification using interpolated Markov models.
    Nucleic Acids Res. 1998 Jan 15;26(2):544-8 PMID: 9421513
  8. Large-scale prokaryotic gene prediction and comparison to genome annotation.
    Bioinformatics. 2005 Dec 15;21(24):4322-9 PMID: 16249266
  9. Recognition of protein coding regions in DNA sequences.
    Nucleic Acids Res. 1982 Sep 11;10(17):5303-18 PMID: 7145702
  10. The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium.
    Proc Natl Acad Sci U S A. 2002 Jul 9;99(14):9509-14 PMID: 12093901
  11. Measurements of the effects that coding for a protein has on a DNA sequence and their use for finding genes.
    Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):551-67 PMID: 6364041
  12. Community structure and metabolism through reconstruction of microbial genomes from the environment.
    Nature. 2004 Mar 4;428(6978):37-43 PMID: 14961025
  13. Finding prokaryotic genes by the 'frame-by-frame' algorithm: targeting gene starts and overlapping genes.
    Bioinformatics. 1999 Nov;15(11):874-86 PMID: 10743554
  14. Improved microbial gene identification with GLIMMER.
    Nucleic Acids Res. 1999 Dec 1;27(23):4636-41 PMID: 10556321
  15. Heuristic approach to deriving models for gene finding.
    Nucleic Acids Res. 1999 Oct 1;27(19):3911-20 PMID: 10481031
  16. Genomic sequencing of Pleistocene cave bears.
    Science. 2005 Jul 22;309(5734):597-9 PMID: 15933159
  17. Combining diverse evidence for gene recognition in completely sequenced bacterial genomes.
    Nucleic Acids Res. 1998 Jun 15;26(12):2941-7 PMID: 9611239
  18. A novel bacterial gene-finding system with improved accuracy in locating start codons.
    DNA Res. 2001 Jun 30;8(3):97-106 PMID: 11475327
  19. Detecting pathogenicity islands and anomalous gene clusters by iterative discriminant analysis.
    FEMS Microbiol Lett. 2003 Apr 25;221(2):269-75 PMID: 12725938
  20. GeneMark.hmm: new solutions for gene finding.
    Nucleic Acids Res. 1998 Feb 15;26(4):1107-15 PMID: 9461475
  21. Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA.
    Science. 2006 Jan 20;311(5759):392-4 PMID: 16368896
  22. GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions.
    Nucleic Acids Res. 2001 Jun 15;29(12):2607-18 PMID: 11410670
  23. Reverse methanogenesis: testing the hypothesis with environmental genomics.
    Science. 2004 Sep 3;305(5689):1457-62 PMID: 15353801
  24. Environmental genome shotgun sequencing of the Sargasso Sea.
    Science. 2004 Apr 2;304(5667):66-74 PMID: 15001713
  25. Modeling and predicting transcriptional units of Escherichia coli genes using hidden Markov models.
    Bioinformatics. 1999 Dec;15(12):987-93 PMID: 10745988
  26. The codon preference plot: graphic analysis of protein coding sequences and prediction of gene expression.
    Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):539-49 PMID: 6694906
  27. The uncultured microbial majority.
    Annu Rev Microbiol. 2003;57:369-94 PMID: 14527284
  28. Comparative metagenomics of microbial communities.
    Science. 2005 Apr 22;308(5721):554-7 PMID: 15845853
  29. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii.
    Science. 1996 Aug 23;273(5278):1058-73 PMID: 8688087
  30. Self-identification of protein-coding regions in microbial genomes.
    Proc Natl Acad Sci U S A. 1998 Aug 18;95(17):10026-31 PMID: 9707594
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkl723
Email
hide@cb.k.u-tokyo.ac.jp
Published
2006-00-00
Epub
2006-00-05
Pages
5623-30
Language
English
Region
England
NLM ID
0411011
PMCID
PMC1636498
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/gkl723 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2