A symmetric-iterated multiple alignment of protein sequences

Journal of Molecular Biology

Volumn 276, Issue 1, 1998, Pages 249-264

  Brocchieri, Luciano ^a   Karlin, Samuel ^a  

^a STANFORD UNIVERSITY   (United States)

Author keywords

Conservation index; Motifs; Multiple alignment; RecA Rad51 RadA

Indexed keywords

ADENOSINE TRIPHOSPHATE; GLYCINE; RECA PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; COMPUTER PROGRAM; CONSENSUS SEQUENCE; DATA BASE; ENZYME CONFORMATION; EUKARYOTE; GENETIC PROCEDURES; MATHEMATICAL COMPUTING; MOLECULAR EVOLUTION; PRIORITY JOURNAL; PROKARYOTE; PROTEIN ANALYSIS; PROTEIN FAMILY; PROTEIN PROTEIN INTERACTION;

ARCHAEA; BACTERIA (MICROORGANISMS); EUKARYOTA; PROKARYOTA;

EID: 0032512801     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.1527     Document Type: Article

References (34)

1. Bailey T.L., Elkan C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology. 1994;28-36
2. Barton G.J., Sternberg M.J.E. Evaluation and improvements in the automatic alignment of protein sequences. Protein Eng. 1:1987;89-94
3. Blaisdell B.E., Rudd K.E., Martin A., Karlin S. Significant dispersed recurrent DNA sequences in the Escherichia coli genome. Several new groups. J. Mol. Biol. 229:1993;833-848
4. Brendel V., Bucher P., Nourbakhsh I.R., Blaisdell B.E., Karlin S. Methods and algorithms for statistical analysis of protein sequences. Proc. Natl Acad. Sci. USA. 89:1992;2002-2006
5. Brendel V., Brocchieri L., Sandler S.J., Clark A.J., Karlin S. Evolutionary comparisons of RecA-like proteins across all major kingdoms of living organisms. J. Mol. Evol. 44:1997;528-541
6. 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. 1978;345-352 Nat. Biomed. Res. Found, Washington, DC
7. Depiereux E., Feytmans E. MATCH-BOX a fundamentally new algorithm for the simultaneous alignment of several protein sequences. Comput. Appl. Biosci. 8:1992;501-509
8. Feng D.-F., Doolittle R.F. Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J. Mol. Evol. 25:1987;351-360
9. Henikoff S., Henikoff J.G. Amino acid substitution matrices from protein blocks. Proc. Natl Acad. Sci. USA. 89:1992;10915-10919
10. Henikoff S., Henikoff J.G. Embedding strategies for effective use of information from multiple sequence alignments. Protein Sci. 6:1997;698-705
11. Henikoff S., Henikoff J.G., Alford W.J., Pietrokovski S. Automated construction and graphical presentation of protein blocks from unaligned sequences. Gene. 163:1995;GC17-GC26
12. Huang X. On global sequence alignment. Comput. Appl. Biosci. 10:1994;227-235
13. Karlin S. Statistical studies of biomolecular sequences score-based methods. Phil. Trans. Roy. Soc. Lond. ser. B. 344:1994;391-402
14. Karlin S., Brocchieri L. Evolutionary conservation of RecA genes in relation to protein structure and function. J. Bacteriol. 178:1996;1881-1894
15. Karlin S., Weinstock G., Brendel V. Bacterial classifications derived from RecA protein sequence comparisons. J. Bacteriol. 177:1995;6881-6893
16. Kowalczykowski S.C., Eggleston A.K. Homologous pairing and DNA strand-exchange proteins. Annu. Rev. Biochem. 63:1994;991-1043
17. Lawrence C.E., Altschul S.F., Boguski M.S., Liu J.S., Neuwald A.F., Wootton J.C. Detecting subtle sequence signals a Gibbs sampling strategy for multiple alignment. Science. 262:1993;208-214
18. Lipman D.J., Altschul S.F., Kececioglu J.D. A tool for multiple alignment. Proc. Natl Acad. Sci. USA. 86:1989;4412-4415
19. McClure M.A., Vasi T.K., Fitch W.M. Comparative analysis of multiple protein-sequence alignment methods. J. Biol. Evol. 11:1994;571-592
20. Needleman S.B., Wunsch C. A general method applicable to the search for similarities in the amino acid sequences of two proteins. J. Mol. Biol. 48:1970;443-453
21. Neuwald A.F., Liu J.S., Lawrence C.E. Gibbs motif sampling detection of bacterial outer membrane protein repeats. Protein Sci. 4:1995;1618-1621
22. Shuler G.D., Altschul S.F., Lipman D.J. A workbench for multiple alignment construction and analysis. Proteins: Struct. Funct. Genet. 9:1991;180-190
23. Smith H.O., Annau T.M., Chandrasegaran S. Finding sequence motifs in groups of functionally related proteins. Proc. Natl Acad. Sci. USA. 87:1990;826-830
24. Smith R.F., Smith T.F. Pattern-induced multi-sequence alignment (PIMA) algorithm employing secondary structure-dependent gap penalties for comparative protein modeling. Protein Eng. 5:1992;35-41
25. Smith, Waterman. Identification of common molecular subsequences. J. Mol. Biol. 147:1981;195-197
26. Smith R.F., Wiese B.A., Wojzynski M.K., Davison D.B., Worley K.C. Search launcher - an integrated interface to molecular biology data base search analysis services available on the world wide web. Genome Res. 6:1996;454-462
27. Story R.M., Weber I.T., Steitz T.A. The structure of the E.coli RecA protein monomer and polymer. Nature. 355:1992;318-325
28. Subbiah S., Harrison S.C. A method for multiple sequence alignment with gaps. J. Mol. Biol. 209:1989;539-548
29. Taylor W.R. Multiple sequence alignment by a pairwise algorithm. Comput. Appl. Biosci. 3:1987;81-87
30. Taylor W.R. A flexible method to align large numbers of biological sequences. J. Mol. Evol. 28:1988;161-169
31. Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl. Acids Res. 22:1994;4673-4680
32. Voloshin O.N., Wang L., Camerini-Otero R.D. Homologous DNA pairing promoted by a 20-amino acid peptide derived from RecA. Science. 272:1996;868-872
33. Walker J.E., Saraste M., Runswick M.J., Gay N.J. Distantly related sequences in the α and β-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J. 1:1982;945-951
34. Waterman M.S., Jones M.S. Consensus methods for DNA and protein sequence alignment. Methods Enzymol. 183:1990;221-237