Further steps in TANGO: Improved taxonomic assignment in metagenomics

Bioinformatics

Volumn 30, Issue 1, 2014, Pages 17-23

  Alonso Alemany, Daniel ^a   Barré, Aurélien ^b   Beretta, Stefano ^c   Bonizzoni, Paola ^c   Nikolski, MacHa ^b   Valiente, Gabriel ^a  

^a UNIVERSITAT POLITÈCNICA DE CATALUNYA   (Spain)

^b UNIVERSITÉ DE BORDEAUX   (France)

^c UNIVERSITY OF MILANO BICOCCA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; CLASSIFICATION; METAGENOMICS; PROCEDURES; SOFTWARE; ARTICLE; COMPUTER PROGRAM; METHODOLOGY;

ALGORITHMS; METAGENOMICS; SOFTWARE;

EID: 84891370765     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt256     Document Type: Article

References (19)

1. Alonso-Alemany, D. et al. (2011) Taxonomic assignment in metagenomics with TANGO. EMBnet. J., 17, 46-50.
2. Altschul, S.F. et al. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
3. Clemente, J.C. et al. (2011) Flexible taxonomic assignment of ambiguous sequencing reads. BMC Bioinformatics, 12, 8.
4. Cole, J.R. et al. (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res., 37, D141-D145.
5. Drö ge, J. and McHardy, A.C. (2012) Taxonomic binning of metagenome samples generated by next-generation sequencing technologies. Brief. Bioinform., 13, 646-655.
6. Federhen, S. (2012) The NCBI taxonomy database. Nucleic Acids Res., 40, D136-D143.
7. Huson, D.H. et al. (2007) MEGAN analysis of metagenomic data. Genome Res., 17, 377-386.
8. Knuth, D.E. (1997) Binary Tree Representation of Trees. In: The Art of Computer Programming. Vol. 1, 3rd edn. Fundamental Algorithms, Reading, Massachusetts: Addison-Wesley, pp. 334-348.
9. Li, W. et al. (2012) Ultrafast clustering algorithms for metagenomic sequence analysis. Brief. Bioinform., 13, 656-668.
10. Mande, S.S. et al. (2012) Classification of metagenomic sequences: methods and challenges. Brief. Bioinform., 13, 669-681.
11. Manichanh, C. et al. (2010) Reshaping the gut microbiome with bacterial transplantation and antibiotic intake. Genome Res., 20, 1411-1419.
12. McDonald, D. et al. (2012) An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J., 6, 610-618.
13. Petrosino, J.F. et al. (2009) Metagenomic pyrosequencing and microbial identification. Clin. Chem., 55, 856-866.
14. Pruitt, K.D. et al. (2012) NCBI reference sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res., 40, D130-D135.
15. Ribeca, P. and Valiente, G. (2011) Computational challenges of sequence classification in microbiomic data. Brief. Bioinform., 12, 614-625.
16. Santamaria, M.B. et al. (2012) Reference databases for taxonomic assignment in metagenomics. Brief. Bioinform., 13, 682-695.
17. Sogin, M.L. et al. (2006) Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc. Natl Acad. Sci. USA, 103, 12115-12120.
18. Stajich, J.E. et al. (2002) The BioPerl toolkit: Perl modules for the life sciences. Genome Res., 12, 1611-1618.
19. Turnbaugh, P.J. et al. (2009) A core gut microbiome in obese and lean twins. Nature, 457, 480-484.