Home LiteratureArticle Details
PMID: 20021646 Published · epublish English Journal Article Research Support, Non-U.S. Gov't

WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads.

BMC bioinformatics ·Vol. 10 ·2009-12-18 ·Pages 430

Gerlach W, Jünemann S, Tille F, Goesmann A, Stoye J

Abstract

Metagenomics is a new field of research on natural microbial communities. High-throughput sequencing techniques like 454 or Solexa-Illumina promise new possibilities as they are able to produce huge amounts of data in much shorter time and with less efforts and costs than the traditional Sanger technique. But the data produced comes in even shorter reads (35-100 basepairs with Illumina, 100-500 basepairs with 454-sequencing). CARMA is a new software pipeline for the characterisation of species composition and the genetic potential of microbial samples using short, unassembled reads. In this paper, we introduce WebCARMA, a refined version of CARMA available as a web application for the taxonomic and functional classification of unassembled (ultra-)short reads from metagenomic communities. In addition, we have analysed the applicability of ultra-short reads in metagenomics. We show that unassembled reads as short as 35 bp can be used for the taxonomic classification of a metagenome. The web application is freely available at http://webcarma.cebitec.uni-bielefeld.de.

MeSH Terms
Computational Biology/methods Genome Genomics/methods Internet Metagenomics/methods Software
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Gerlach Wolfgang
Faculty of Technology, Bielefeld University, Bielefeld, Germany. wolfgang.gerlach@cebitec.uni-bielefeld.de
Jünemann Sebastian
Tille Felix
Goesmann Alexander
Stoye Jens
References (35)
35 references, click to expand
  1. TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences.
    BMC Bioinformatics. 2004 Oct 26;5:163 PMID: 15507136
  2. Substantial biases in ultra-short read data sets from high-throughput DNA sequencing.
    Nucleic Acids Res. 2008 Sep;36(16):e105 PMID: 18660515
  3. Community structure and metabolism through reconstruction of microbial genomes from the environment.
    Nature. 2004 Mar 4;428(6978):37-43 PMID: 14961025
  4. The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes.
    BMC Bioinformatics. 2008 Sep 19;9:386 PMID: 18803844
  5. Metagenomics for studying unculturable microorganisms: cutting the Gordian knot.
    Genome Biol. 2005;6(8):229 PMID: 16086859
  6. Metagenomics: read length matters.
    Appl Environ Microbiol. 2008 Mar;74(5):1453-63 PMID: 18192407
  7. Accurate whole human genome sequencing using reversible terminator chemistry.
    Nature. 2008 Nov 6;456(7218):53-9 PMID: 18987734
  8. The metagenome of a biogas-producing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology.
    J Biotechnol. 2008 Aug 31;136(1-2):77-90 PMID: 18597880
  9. MEGAN analysis of metagenomic data.
    Genome Res. 2007 Mar;17(3):377-86 PMID: 17255551
  10. Genetic diversity in Sargasso Sea bacterioplankton.
    Nature. 1990 May 3;345(6270):60-3 PMID: 2330053
  11. Genomic analysis of uncultured marine viral communities.
    Proc Natl Acad Sci U S A. 2002 Oct 29;99(22):14250-5 PMID: 12384570
  12. Environmental genome shotgun sequencing of the Sargasso Sea.
    Science. 2004 Apr 2;304(5667):66-74 PMID: 15001713
  13. Database resources of the National Center for Biotechnology Information.
    Nucleic Acids Res. 2009 Jan;37(Database issue):D5-15 PMID: 18940862
  14. Characterizing the mouse ES cell transcriptome with Illumina sequencing.
    Genomics. 2008 Oct;92(4):187-94 PMID: 18602984
  15. The neighbor-joining method: a new method for reconstructing phylogenetic trees.
    Mol Biol Evol. 1987 Jul;4(4):406-25 PMID: 3447015
  16. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
    Nat Genet. 2000 May;25(1):25-9 PMID: 10802651
  17. GenBank.
    Nucleic Acids Res. 2009 Jan;37(Database issue):D26-31 PMID: 18940867
  18. Comparative metagenomics of microbial communities.
    Science. 2005 Apr 22;308(5721):554-7 PMID: 15845853
  19. Bacterial evolution.
    Microbiol Rev. 1987 Jun;51(2):221-71 PMID: 2439888
  20. TACOA: taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach.
    BMC Bioinformatics. 2009 Feb 11;10:56 PMID: 19210774
  21. Phylogenetic structure of the prokaryotic domain: the primary kingdoms.
    Proc Natl Acad Sci U S A. 1977 Nov;74(11):5088-90 PMID: 270744
  22. Genome signature comparisons among prokaryote, plasmid, and mitochondrial DNA.
    Proc Natl Acad Sci U S A. 1999 Aug 3;96(16):9184-9 PMID: 10430917
  23. Rapid identification of genes encoding DNA polymerases by function-based screening of metagenomic libraries derived from glacial ice.
    Appl Environ Microbiol. 2009 May;75(9):2964-8 PMID: 19270136
  24. The Pfam protein families database.
    Nucleic Acids Res. 2008 Jan;36(Database issue):D281-8 PMID: 18039703
  25. Profile hidden Markov models.
    Bioinformatics. 1998;14(9):755-63 PMID: 9918945
  26. Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas reactor.
    J Biotechnol. 2008 Aug 31;136(1-2):91-101 PMID: 18611419
  27. Phylogenetic classification of short environmental DNA fragments.
    Nucleic Acids Res. 2008 Apr;36(7):2230-9 PMID: 18285365
  28. Compositional biases of bacterial genomes and evolutionary implications.
    J Bacteriol. 1997 Jun;179(12):3899-913 PMID: 9190805
  29. Microbial ecology of four coral atolls in the Northern Line Islands.
    PLoS One. 2008 Feb 27;3(2):e1584 PMID: 18301735
  30. Single-molecule sequencing of an individual human genome.
    Nat Biotechnol. 2009 Sep;27(9):847-50 PMID: 19668243
  31. Novel phylogenetic studies of genomic sequence fragments derived from uncultured microbe mixtures in environmental and clinical samples.
    DNA Res. 2005;12(5):281-90 PMID: 16769690
  32. Baselines and degradation of coral reefs in the Northern Line Islands.
    PLoS One. 2008 Feb 27;3(2):e1548 PMID: 18301734
  33. Accurate phylogenetic classification of variable-length DNA fragments.
    Nat Methods. 2007 Jan;4(1):63-72 PMID: 17179938
  34. Basic local alignment search tool.
    J Mol Biol. 1990 Oct 5;215(3):403-10 PMID: 2231712
  35. Identification of protein coding regions by database similarity search.
    Nat Genet. 1993 Mar;3(3):266-72 PMID: 8485583
Article Info
Journal
BMC bioinformatics
Abbr.
BMC Bioinformatics
ISSN
1471-2105
DOI
10.1186/1471-2105-10-430
Email
wolfgang.gerlach@cebitec.uni-bielefeld.de
Published
2009-12-18
Epub
2009-00-18
Pages
430
Language
English
Region
England
NLM ID
100965194
PMCID
PMC2801688
Subset
IM
External Links
PubMed source DOI: 10.1186/1471-2105-10-430 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