CoMet - A web server for comparative functional profiling of metagenomes

Nucleic Acids Research

Volumn 39, Issue SUPPL. 2, 2011, Pages

  Lingner, Thomas ^a   Aßhauer, Kathrin Petra ^a   Schreiber, Fabian ^a,b   Meinicke, Peter ^a  

^a UNIVERSITY OF GÖTTINGEN   (Germany)

^b STOCKHOLM UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR PFAM; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; CLIENT SERVER APPLICATION; CLUSTER ANALYSIS; COMPARATIVE GENOMIC HYBRIDIZATION; COMPUTER INTERFACE; GENE FUNCTION; GENE SEQUENCE; GENETIC ANALYSIS; HIGH THROUGHPUT SCREENING; MATHEMATICAL ANALYSIS; MEDICAL RESEARCH; METAGENOME; OPEN READING FRAME; PRIORITY JOURNAL; PROTEIN DOMAIN;

CLUSTER ANALYSIS; DATA INTERPRETATION, STATISTICAL; INTERNET; METAGENOME; METAGENOMICS; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ANALYSIS, DNA; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

EID: 79960030549     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr388     Document Type: Article

References (24)

1. Daniel, R. (2005) The metagenomics of soil. Nat. Rev. Microbiol., 3, 470-478. (Pubitemid 40716173)
2. Tringe, S.G., von Mering, C., Kobayashi, A., Salamov, A.A., Chen, K., Chang, H.W., Podar, M., Short, J.M., Mathur, E.J., Detter, J.C. et al. (2005) Comparative metagenomics of microbial communities. Science, 308, 554-557. (Pubitemid 40570586)
3. Turnbaugh, P.J., Hamady, M., Yatsunenko, T., Cantarel, B.L., Duncan, A., Ley, R.E., Sogin, M.L., Jones, W.J., Roe, B.A., Affourtit, J.P. et al. (2009) A core gut microbiome in obese and lean twins. Nature, 457, 480-484.
4. Tatusov, R.L., Fedorova, N.D., Jackson, J.D., Jacobs, A.R., Kiryutin, B., Koonin, E.V., Krylov, D.M., Mazumder, R., Mekhedov, S.L., Nikolskaya, A.N. et al. (2003) The COG database: an updated version includes eukaryotes. BMC Bioinformatics, 4, 41.
5. Meyer, F., Overbeek, R. and Rodriguez, A. (2009) FIGfams: yet another set of protein families. Nucleic Acids Res., 37, 6643-6654.
6. Finn, R.D., Mistry, J., Tate, J., Coggill, P., Heger, A., Pollington, J.E., Gavin, O.L., Gunasekaran, P., Ceric, G., Forslund, K. et al. (2010) The Pfam protein families database. Nucleic Acids Res., 38, D211-D222.
7. Meyer, F., Paarmann, D., D'Souza, M., Olson, R., Glass, E.M., Kubal, M., Paczian, T., Rodriguez, A., Stevens, R., Wilke, A. et al. (2008) The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics, 9, 386.
8. Aoki-Kinoshita, K.F. and Kanehisa, M. (2007) Gene annotation and pathway mapping in KEGG. Methods Mol. Biol., 396, 71-91. (Pubitemid 350190035)
9. Li, W. (2009) Analysis and comparison of very large metagenomes with fast clustering and functional annotation. BMC Bioinformatics, 10, 359.
10. Seshadri, R., Kravitz, S.A., Smarr, L., Gilna, P. and Frazier, M. (2007) CAMERA: a community resource for metagenomics. PLoS Biol., 5, e75.
11. Gerlach, W., Junemann, S., Tille, F., Goesmann, A. and Stoye, J. (2009) WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads. BMC Bioinformatics, 10, 430.
12. Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S. and Eppig, J.T. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29. (Pubitemid 30257031)
13. Markowitz, V.M., Ivanova, N.N., Szeto, E., Palaniappan, K., Chu, K., Dalevi, D., Chen, I.M., Grechkin, Y., Dubchak, I., Anderson, I. et al. (2008) IMG/M: a data management and analysis system for metagenomes. Nucleic Acids Res., 36, D534-D538. (Pubitemid 351149780)
14. Goll, J., Rusch, D.B., Tanenbaum, D.M., Thiagarajan, M., Li, K., Methe, B.A. and Yooseph, S. (2010) METAREP: JCVI metagenomics reports-an open source tool for high-performance comparative metagenomics. Bioinformatics, 26, 2631-2632.
15. Kottmann, R., Kostadinov, I., Duhaime, M.B., Buttigieg, P.L., Yilmaz, P., Hankeln, W., Waldmann, J. and Glö ckner, F.O. (2010) Megx.net: integrated database resource for marine ecological genomics. Nucleic Acids Res., 38, D391-D395.
16. Hoff, K.J., Tech, M., Lingner, T., Daniel, R., Morgenstern, B. and Meinicke, P. (2008) Gene prediction in metagenomic fragments: a large scale machine learning approach. BMC Bioinformatics, 9, 217.
17. Meinicke, P. (2009) UFO: a web server for ultra-fast functional profiling of whole genome protein sequences. BMC Genomics, 10, 409.
18. Lingner, T. and Meinicke, P. (2008) Word correlation matrices for protein sequence analysis and remote homology detection. BMC Bioinformatics, 9, 259.
19. Rodriguez-Brito, B., Rohwer, F. and Edwards, R.A. (2006) An application of statistics to comparative metagenomics. BMC Bioinformatics, 7, 162.
20. Torgerson, W. (1952) Multidimensional scaling: I. Theory and method. Psychometrika, 17, 401-419.
21. Dinsdale, E.A., Edwards, R.A., Hall, D., Angly, F., Breitbart, M., Brulc, J.M., Furlan, M., Desnues, C., Haynes, M. and Li, L. (2008) Functional metagenomic profiling of nine biomes. Nature, 452, 629-632. (Pubitemid 351483360)
22. Schreiber, F., Gumrich, P., Daniel, R. and Meinicke, P. (2010) Treephyler: fast taxonomic profiling of metagenomes. Bioinformatics, 26, 960-961.
23. Kunin, V., Raes, J., Harris, J.K., Spear, J.R., Walker, J.J., Ivanova, N., von Mering, C., Bebout, B.M., Pace, N.R., Bork, P. et al. (2008) Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat. Mol. Syst. Biol., 4, 198.
24. Marchler-Bauer, A., Panchenko, A.R., Shoemaker, B.A., Thiessen, P.A., Geer, L.Y. and Bryant, S.H. (2002) CDD: a database of conserved domain alignments with links to domain three-dimensional structure. Nucleic Acids Res., 30, 281-283. (Pubitemid 34679564)