Database similarity searches

Methods in Molecular Biology

Volumn 484, Issue , 2008, Pages 361-378

  Plewniak, Frédéric ^a  

^a INSTITUT DE GÉNÉTIQUE ET DE BIOLOGIE MOLÉCULAIRE ET CELLULAIRE   (France)

Author keywords

Database; Homology; Search; Sequence alignment; Sequence comparison; Similarity

Indexed keywords

PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; GENETICS; METHODOLOGY; MOLECULAR GENETICS; PROTEIN DATABASE; REVIEW; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY;

ALGORITHMS; AMINO ACID SEQUENCE; DATABASES, PROTEIN; MOLECULAR SEQUENCE DATA; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 60349101061     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-59745-398-1_24     Document Type: Review

References (15)

1. Rao, J. K. M. (1987) New scoring matrix for amino acid residue exchange based on residue characteristic physical parameters. Int. J. Peptide Protein Res. 29, 276-281.
2. Henikoff, S. and Henikoff, J. G. (1993) Performance evaluation of amino acid substitution matrices. Proteins: Structure Function Genet. 17, 49-61.
3. Henikoff, S. and Henikoff, J. G. (1992) Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA 89, 10915-10919.
4. Dayhoff, M. O., Schwartz, R. M., and Orcutt, B. C. (1978) A model of evolutionary change in proteins. Atlas Protein Sequence Struct. 5, 345-352.
5. Altschul, S. F., Madden, T. L., Schaeffer, A. A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
6. Pearson, W. R. and Lipman, D. J. (1988) Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. USA 85, 2444-2448.
7. Gumbel, E. J. (1958) Statistics of Extremes. Columbia University Press, New York.
8. Needleman, S. B and Wunsch, C. D. (1970) A general method applicable to the search for similarities in the amino acid sequences of two proteins. J. Mol. Biol. 48, 443-453.
9. Smith, T. F. and Waterman, M. S. (1981) Identification of common molecular subsequences. J. Mol. Biol. 147, 195-197.
10. The UniProt Consortium. (2007) The Universal Protein Resource (UniProt). Nucleic Acids Res. 35, D193-D197.
11. Pruitt, K. D., Tatusova, T., and Maglott, D. R. (2007) NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 35, D61-D65.
12. Berman, H. M., Battistuz, T., Bhat, T. N., Bluhm, W. F., Bourne, P. E., Burkhardt, K., Feng, Z., Gilliland, G. L., Iype, L., Jain, S., Fagan, P., Marvin, J., Padilla, D., Ravichandran, V., Schneide, B., Thanki, N., Weissig, H., Westbrook, J. D., and Zardecki, C. (2002) The Protein Data Bank. Acta Crrystallogr. D Biol. Crystallogr. 58, 899-907.
13. Suzek, B. E., Huang, H., McGarvey, P., Mazumder, R., and Wu, C. H. (2007) UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics 23, 282-288.
14. Wootton, J. C. and Federhen, S. (1993) Statistics of local complexity in amino acid sequences and sequence databases. Comput. Chem. 17, 149-163.
15. Bateman, A., Coin, L., Durbin, R., Finn, R. D., Hollich, V., Griffiths-Jones, S., Khanna, A., Marshall, M., Moxon, S., Sonnhammer, E. L., Studholme, D. J., Yeats, C., and Eddy, S. R. (2004) The Pfam protein families database. Nucleic Acids Res. 32, D138-D141.