Using BLOSUM in sequence alignments

Cold Spring Harbor Protocols

Volumn 3, Issue 6, 2008, Pages

  Mount, David W ^a  

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ALGORITHM; AMINO ACID ANALYSIS; AMINO ACID SUBSTITUTION; ARTICLE; COMPUTER PROGRAM; FREQUENCY ANALYSIS; MATHEMATICAL ANALYSIS; MATHEMATICAL COMPUTING; MOLECULAR EVOLUTION; MOLECULAR MODEL; PROCESS OPTIMIZATION; PROTEIN DATABASE; PROTEIN DOMAIN; SCORING SYSTEM; SEQUENCE ALIGNMENT;

EID: 55249096440     PISSN: None     EISSN: 15596095     Source Type: Journal    
DOI: 10.1101/pdb.top39     Document Type: Article

References (10)

1. Bairoch, A. 1991. PROSITE: A dictionary of sites and patterns in proteins. Nucleic Acids Res. 19: 2241-2245.
2. Henikoff, S. and Henikoff, J.G. 1991. Automated assembly of protein blocks for database searching. Nucleic Acids Res. 19: 6565-6572.
3. Henikoff, S. and Henikoff, J.G. 1992. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. 89: 10915-10919.
4. Henikoff, S. and Henikoff, J.G. 1993. Performance evaluation of amino acid substitution matrices. Proteins Struct. Funct. Genet. 17: 49-61.
5. Mount, D.W. 2008a. Using PAM matrices in sequence alignments. CSH Protocols (this issue) doi: 10.1101/pdb.top38.
6. Mount, D.W. 2008b. Comparison of the PAM and BLOSUM amino acid substitution matrices. CSH Protocols (this issue) doi: 10.1101/ pdb.ip59.
7. Mount, D.W. 2008c. A test of the Markov model of evolution in proteins. CSH Protocols (this issue) doi: 10.1101/pdb.ip58.
8. Mount, D.W. 2008d. Using gaps and gap penalties to optimize pairwise sequence alignments. CSH Protocols (this issue) doi: 10.1101/ pdb.top40.
9. Mount, D.W. 2008e. Studies of varying alignment algorithm, amino acid scoring matrix and gap penalties. CSH Protocols (this issue) doi: 10.1101/pdb.ip60.
10. Smith, H.O., Annau, T.M., and Chandrasegaran, S. 1990. Finding sequence motifs in groups of functionally related proteins. Proc. Natl. Acad. Sci. 87: 826-830