DivergentSet, a tool for picking non-redundant sequences from large sequence collections

Molecular and Cellular Proteomics

Volumn 5, Issue 8, 2006, Pages 1520-1532

  Widmann, Jeremy ^a   Hamady, Micah ^b   Knight, Rob ^a  

^a UNIVERSITY OF COLORADO   (United States)

^b University of Colorado   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID;

AMINO ACID SEQUENCE; ARTICLE; BIOINFORMATICS; COMPUTER INTERFACE; COMPUTER PROGRAM; COMPUTER SYSTEM; CONTROLLED STUDY; ENTROPY; ONLINE SYSTEM; PRIORITY JOURNAL; PROTEIN MOTIF; SENSITIVITY ANALYSIS;

AMINO ACID SEQUENCE; COMPUTATIONAL BIOLOGY; MOLECULAR SEQUENCE DATA; PATTERN RECOGNITION, AUTOMATED; PHYLOGENY; SEQUENCE ANALYSIS; SOFTWARE;

EID: 33748309025     PISSN: 15359476     EISSN: None     Source Type: Journal    
DOI: 10.1074/mcp.T600022-MCP200     Document Type: Article

References (23)

1. Bailey, T. L., and Elkan, C. (1994) in ISMB-94: Proceedings, Second International Conference on Intelligent Systems for Molecular Biology (Altman, R., Brutlag, D., Karp, P., and Searls, D., eds) pp. 28-36, AAAI Press, Menlo Park, CA
2. Lockless, S., and Ranganathan, R. (1999) Evolutionarily conserved pathways of energetic connectivity in protein families. Science 286, 295-299
3. Copley, S., and Dhillon, J. (2002) Lateral gene transfer and parallel evolution in the history of glutathione biosynthesis genes. Genome Biol. 3, Research0025
4. Copley, S., Novak, W., and Babbitt, P. (2004) Divergence of function in the thioredoxin fold suprafamily: evidence for evolution of peroxiredoxins from a thioredoxin-like ancestor. Biochemistry 43, 13981-13995
5. Tamura, K., Nei, M., and Kumar, S. (2004) Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc. Natl. Acad. Sci. U. S. A. 101, 11030-11035
6. Poe, S. (1998) Sensitivity of phylogeny estimation to taxonomic sampling. Syst. Biol. 47, 18-31
7. Rosenberg, M., and Kumar, S, (2001) Incomplete taxon sampling is not a problem for phylogenetic inference. Proc. Natl. Acad. Sci. U. S. A. 98, 10751-10756
8. Altschul, S., Gish, W., Miller, W., Myers, E., and Lipman, D. (1990) Basic local alignment search tool. J. Mol. Biol. 215, 403-410
9. Holm, L., and Sander, C. (1998) Removing near-neighbour redundancy from large protein sequence collections. Bioinformatics 14, 423-429
10. Schloss, P., and Handelsman, J. (2005) Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness, Appl. Environ. Microbiol. 71, 1501-1506
11. Seguritan, V., and Rowher, F. (2001) Fastgroup: a program to dereplicate libraries of 16S rDNA sequences. BMC Bioinformatics 2, 9
12. Bernstein, F., Koetzle, T., Williams, G., Meyer, E. F., J., Brice, M., Rodgers, J., Kennard, O., Shimanouchi, T., and Tasumi, M. (1977) The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535-542
13. Altschul, S., Madden, T., Schaffer, A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402
14. Pegg, S., and Babbitt, P. (1999) Shotgun: getting more from sequence similarity searches. Bioinformatics 15, 729-740
15. Needleman, S., and Wunsch, C. (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48, 443-453
16. Dice, L. (1945) Measures of the amount of ecologic association between species. Ecology 26, 297-302
17. Edgar, R. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792-1797
18. Sneath, P., and Sokal, R. (1973) Numerical Taxonomy, Freeman, San Francisco
19. Saitou, N., and Nei, M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425
20. Matsumoto, M., and Nishimura, T. (1998) Mersenne Twister: a 623-dimensionally equidistributed uniform pseudorandom number generator. ACM Trans. Model. Comput. Simul. 8, 3-30
21. Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., and Kanehisa, M. (1999) KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 27, 29-34
22. Ibba, M., Morgan, S., Curnow, A., Pridmore, D., Vothknecht, U., Gardner, W., Lin, W., Woese, C., and Soll, D. (1997) A euryarchaeal lysyl-tRNA synthetase: resemblance to class I synthetases. Science 278, 1119-1122
23. Page, R. (1993) On describing the shape of rooted and unrooted trees. Cladistics 9, 93-99