Evidence-based clustering of reads and taxonomic analysis of metagenomic data

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 5780 LNBI, Issue , 2009, Pages 102-112

  Folino, Gianluigi ^a   Gori, Fabio ^b   Jetten, Mike S M ^b   Marchiori, Elena ^b  

^a ICAR CNR   (Italy)

^b RADBOUD UNIVERSITY NIJMEGEN   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

BENCHMARK DATASETS; CLASS LEVEL; CLUSTERING ANALYSIS; CLUSTERING METHODS; COMPARATIVE ANALYSIS; DATA ANALYSIS; DATA SETS; INTERNAL STRUCTURE; METAGENOMICS; PARTIAL SEQUENCES; PROTEIN FAMILY; RELATIVE ABUNDANCE;

BIOINFORMATICS; CLUSTER ANALYSIS; PATTERN RECOGNITION; TAXONOMIES;

CLUSTERING ALGORITHMS;

EID: 70349850646     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-04031-3_10     Document Type: Conference Paper

References (14)

1. Yooseph, S., et al.: The Sorcerer II global ocean sampling expedition: Expanding the universe of protein families. PLoS Biol. 5(3), e16 (2007)
2. McHardy, A., Rigoutsos, I.: What's in the mix: phylogenetic classification of metagenome sequence samples. Current Opinion inMicrobiology 10, 499-503 (2007)
3. Raes, J., Foerstner, K., Bork, P.: Get the most out of your metagenome: computational analysis of environmental sequence data. Current Opinion in Microbiology 10, 490-498 (2007)
4. Li, W., Wooley, J., Godzik, A.: Probing metagenomics by rapid cluster analysis of very large datasets. PLoS One 3(10) (2008)
5. Dalevi, D., Ivanova, N., Mavromatis, K., Hooper, S., Szeto, E., Hugenholtz, P., Kyrpides, N., Markowitz, V.: Annotation of metagenome short reads using proxygenes. Bioinformatics 24(16) (2008)
6. Pop, M., Phillippy, A., Delcher, A., Salzberg, S.: Comparative genome assembly. Briefings in Bioinformatics 5(3), 237-248 (2004)
7. Chan, C., Hsu, A., Tang, S., Halgamuge, S.: Using growing self-organising maps to improve the binning process in environmental whole-genome shotgun sequencing. Journal of Biomedicine and Biotechnology (2008)
8. Folino, G., Gori, F., Jetten, M.S.M., Marchiori, E.: Clustering metagenome short reads using weighted proteins. In: EvoBIO 2009. LNCS, vol.5483, pp. 152-163. Springer, Heidelberg (2009)
9. Korf, I., Yandell, M., Bedell, J.: BLAST. O'Reilly & Associates, Inc., Sebastopol (2003)
10. Madden, T.: 16. In: The BLAST Sequence Analysis Tool, Bethesda, MD (2002)
11. Altschul, S., Gish, W., Miller, W., Myers, E., Lipman, D.: Basic local alignment search tool. J. Molecular Biology 215(3), 403-410 (1990)
12. Marchiori, E., Steenbeek, A.: An evolutionary algorithm for large scale set covering problems with application to airline crew scheduling. In: Oates, M.J., et al. (eds.) EvoIASP 2000, EvoWorkshops 2000, EvoFlight 2000, EvoSCONDI 2000, EvoSTIM 2000, EvoTEL 2000, and EvoROB/EvoRobot 2000. LNCS, vol.1803, pp. 367-381. Springer, Heidelberg (2000)
13. Biddle, J.F., et al.: Metagenomic signatures of the Peru margin subsea.oor biosphere show a genetically distinct environment. PNAS (105), 10583-10588 (2008)
14. Venter, J., et al.: Environmental genome shotgun sequencing of the sargasso sea. Science (304), 66-74 (2004)