Dynamic sequence databank searching with templates and multiple alignment

Journal of Molecular Biology

Volumn 280, Issue 3, 1998, Pages 375-406

  Taylor, William R ^a  

^a The Ridgeway Mill Hill NW7 1AA   (United Kingdom)

Author keywords

Multiple alignment; Sequence databank searching; Templates

Indexed keywords

ALGORITHM; ARTICLE; COMPUTER PROGRAM; DATA BASE; DNA TEMPLATE; GENETIC PROCEDURES; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SCINTISCANNING;

EID: 0032540981     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.1853     Document Type: Article

References (25)

1. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 214:1990;403-410
2. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J.H., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-blast a new generation of protein database search programs. Nucl. Acids Res. 25:1997;3389-3402
3. Bairoch A., Boeckmann B. The SWISS-PROT protein sequence data bank. Nucl. Acids Res. 19:1991;2247-2249
4. Bajaj M., Waterfield M., Schlessinger J., Taylor W.R., Blundell T.L. On the tertiary struc tures of the extracellular domains of the EGF and insulin receptors. Biochim. Biophys. Acta. 916:1987;220-226
5. Barton G.J., Sternberg M.J.E. Flexible protein sequence patterns a sensitive method to detect weak structural similarities. J. Mol. Biol. 212:1990;389-402
6. Bashford D., Chothia C., Lesk A.M. Determinants of a protein fold-unique features of the globin amino-acid sequences. J. Mol. Biol. 196:1987;199-216
7. Higgins D.G., Sharp P.M. Clustal a package for performing multiple sequence alignment on a microcomputer. Gene. 73:1988;237-244
8. Holm L., Sander C. Globin fold in a bacterial toxin. Nature. 361:1993;309
9. Jones D.T., Taylor W.R., Thornton J.M. A new approach to protein fold recognition. Nature. 358:1992;86-89
10. Murphy M.E.P., Lindley P.F., Adman E.T. Structural comparison of cupredoxin domains domain recycling to construct proteins with novel functions. Protein Sci. 6:1997;761-770
11. Neuwald A.F., Liu J.S., Lipman D.J., Lawrence C.E. Extracting protein alignment models from the sequence database. Nucl. Acids Res. 25:1997;1665-1677
12. Orengo C.A., Taylor W.R. A local alignment method for protein structure motifs. J. Mol. Biol. 233:1993;488-497
13. Pearl L.H., Taylor W.R. A structural model for the retroviral proteases. Nature. 329:1987;351-354
14. Pearson W.R. Rapid and sensitive sequence comparison with FASTP and FASTA. Doolittle R.F. Methods in Enzymology. vol. 183:1990;63-98 Academic Press, Inc, San Diego, CA. chapt. 5
15. Smith R.F., Smith T.F. Automatic generation of primary sequence patterns from sets of related protein sequences. Proc. Natl Acad. Sci USA. 87:1990;118-122
16. Smith T.F., Waterman M.S. Identification of common molecular subsequences. J. Mol. Biol. 147:1981;195-197
17. Taylor W.R. The classification of amino acid conservation. J. Theor. Biol. 119:1986;205-218
18. Taylor W.R. Identification f protein sequence homology by consensus template alignment. J. Mol. Biol. 188:1986;233-258
19. Taylor W.R. A flexible method to align large numbers of biological sequences. J. Mol. Evol. 28:1988;161-169
20. Taylor W.R. A template based method of pattern matching in protein sequences. Prog. Biophys. Mol. Biol. 54:1989;159-252
21. Taylor W.R. Multiple protein sequence alignment algorithms for gap insertion. Doolittle R.F. Methods in Enzymology. vol. 266:1996;343-367 Academic Press, Orlando, FA
22. Taylor W.R. Multiple sequence threading an analysis of alignment quality and stability. J. Mol. Biol. 269:1997;902-943
23. Walker J.E., Saraste M., Runswick W.J., Gay N.J. Distantly related sequences in the α-subunits and β-subunits of ATP synthase, myosin, kinases and other ATP requiring enzymes and a common nucleotide binding fold. EMBO J. 1:1992;945-951
24. Dayhoff M.O., Schwartz R.M., Orcutt B.C. A model of evolutionary change in proteins. Dayhoff M.O. Atlas of Protein Sequence and Structure. vol. 5:1978;345-352 Natl Biomed. Res. Found, Washington, DC. suppl. 5
25. Taylor W.R. A flexible method to align large numbers of biological sequences. J. Mol. Evol. 28:1988;161-169