Match-box_server: A multiple sequence alignment tool placing emphasis on reliability

Bioinformatics

Volumn 13, Issue 3, 1997, Pages 249-256

  Depiereux, Eric ^a   Baudoux, Guy ^a   Briffeuil, Pascal ^a   Reginster, Isabelle ^a   De Bolle, Xavier ^a   Vinals, Carla ^a   Feytmans, Ernest ^a  

^a UNIVERSITY OF NAMUR   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

OLIGONUCLEOTIDE;

AMINO ACID SEQUENCE; ARTICLE; COMPUTER PROGRAM; GENETIC PROCEDURES; MUTAGENESIS; POLYMERASE CHAIN REACTION; PREDICTION; PRIORITY JOURNAL; PROTEIN FAMILY; PROTEIN STRUCTURE; RELIABILITY; SCORING SYSTEM;

ALGORITHMS; AMINO ACID SEQUENCE; ANIMALS; ASPARTIC ENDOPEPTIDASES; CONSERVED SEQUENCE; HUMANS; MOLECULAR SEQUENCE DATA; PROTEINS; REPRODUCIBILITY OF RESULTS; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; SOFTWARE;

EID: 0030996742     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/13.3.249     Document Type: Article

References (34)

1. Altschul.S.F., Gish.W., Miller.W.. Myers.E.W. and Lipman.D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215. 403-410.
2. Argos.P. (1987) A sensitive procedure to compare amino acid sequences. J. Mol. Biol., 193, 385-396.
3. Bailey.T.L. and Elkan.C. (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. In: Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology. AAAI Press. Menlo Park, CA, pp. 28-36.
4. Barton.G.J. and Sternberg.M.J.E. (1987) A strategy for the rapid multiple alignment of protein sequences. J. Mol. Biol., 198, 327-337.
5. Bertrand.L., Vertommen.D., Depiereux.E., Hue.L.. Rider.M.H. and Feytmans.E. (1997) Modelling the 2-kinase domain of 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase on adenylate kinase. J. Biochem., 321, 615-621.
6. Bordo.D., Djinovic.K. and Bolognesi.M. (1994) Conserved patterns in the Cu.Zn superoxide dismutase family. J. Mol. Biol., 238, 366-386.
7. De Bolle, X., Vinals, C, Prozzi, D., Paquet, J.Y., Leplae, R., Depiereux, E., Vandenhaute, J. and Feytmans, E. (1995) Identification of residues potentially involved in the interactions between subunits in yeast alcohol dehydrogenases. Eur. J. Biochem., 231, 214-219.
8. Delforge, D., Depiereux.E., De Bolle.X., Feytmans.E. and Remacle.J. (1993) Similarities between alanine dehydrogenase and the N-terminal part of pyndine nucleotide transhydrogenase and their possible implication in the virulence mechanism of Mycobacterium tuberculosis. Biochem. Biophys. Res. Commun., 190, 1073-1079.
9. Depiereux.E. and Feytmans.E. (1991) Simultaneous and multivariate alignment of protein sequences—Correspondence between physicochemical profiles and structurally conserved regions (SCR). Protein Eng., 4, 603-613.
10. Depiereux.E. and Feytmans.E. (1992) MATCH-BOX—A fundamentally new algorithm for the simultaneous alignment of several protein sequences. Comput. Applic. Biosci., 8, 501-509.
11. Feng.D.F. and Doolittle.R.F. (1987) Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J. Mol. Evoi, 25, 351-360.
12. Greer.J. (1990) Comparative modelling methods—application to the family of the mammalian serine proteases. Protein Struct. Fund. Genet., 7, 317— 334.
13. Henikoff.S. and Henikoff.J.G. (1992) Amino acid subslitution matrices from protein blocks. Proc. Nail Acad. Sci. USA. 89. 10915-10919.
14. Holm.L., Ouzounis.C, Sander.C. Tuparev.G. and Vriend.G. (1992) A database of protein structure families with common folding motif. Protein Sci.. 1. 1691-1693.
15. Huang, X. (1994) On global sequence alignment. Comput. Applic. Biosci.. 10, 227-235.
16. Lawrence.C.E.. Altschul.S.F., Boguski.M.S., Liu.J.S., Neuwald.A F and WootonJ.C. (1993) Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science. 268, 208-214.
17. Lipman.D.J.. Altschul.S.F. and Kececioglu.J.D. (1989) A tool for multiple sequence alignment. Proc. Natl Acad. Sci. USA. 86, 4412-4415.
18. McKenzie.H.A. and White.F.H. (1991) Lysozyme and alpha-lactalbumin: structure, function and interrelationship. Adv. Protein Chem.. 41, 173-315.
19. Mosimann.S., Meleshko.R. and James.M.N.G. (1995) A critical assessment of comparative molecular modelling of tertiary structures of proteins. Protein Struct. Fund. Genet., 23, 301-318.
20. Newman, M., Watson, F., Roychowdhury, P., Jones, H., Badassc, M., Cleasby, A., Wood, S.P., Tickle, U. and Blundell, T.L. (1993) X-ray analyses of aspartic proteinases. V. Structure and refinement at 2.0 A resolution of the aspartic proteinase from Mucor pusillus. J. Mol. Bioi, 230, 260-283.
21. Pastore, A. and Lesk, A M. (1990) Comparisons of the structures of globins and phycocyanins: evidence fo revolutionary relationship. Prot. Struct. Fund. Gen.. 8, 133-155
22. Schuler, G.D., Altschul, S.F. and Lipman, D.J. (1991) A workbench for multiple alignment construction and analysis. Protein Struct. Fund. Genet.. 9. 180-190.
23. Siezen.R.J., de Vos.W M.. Leunissen.J.A M. and Dijkstra.B.W. (1991) Homology modelling and protein engineering strategy of subtilases, the family of subtilisin-like serine proteinases. Protein Eng.. 4. 719-737.
24. Smith, H.O., Annau.T.M. and Chandrasegaran.S. (1990) Finding sequence motifs in groups of functionally related proteins. Proc. Natl Acad. Sci. USA. 87, 826-830.
25. Smith.R.F. and Smith.T.F. (1992) Pattern-induced multi-sequence alignment (PIMA) algorithm employing secondary structure-dependent gap penalties for use in comparative protein modelling. Protein Eng., 5, 35-41
26. Sneath, P.H.A. and Sokal, R.R. (1973) Numerical Taxonomy. Freeman, San Francisco. CA.
27. Subbiah.S. and Harrison, S.C. (1989) A method for multiple sequence alignment with gaps. J. Mol. Bioi, 209. 539-548.
28. Taylor, W.R (1988) A flexible method to align large numbers of biological sequences. J. Mol. Evol., 28, 161-169.
29. Thompson.J.D., Higgins.D.G. and Gibson.T.J (1994) CLUSTALW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 11, 4673-4680.
30. Tibor.A., Weynants.V., Denoel.P., Lichtfouse.B.. De Bolle.X.. Saman.E.. LimetJ.N. and Letesson.J.J. (1994) Molecular cloning, nucelotide sequence, and occurence of a 16.5-kilodalton outer membrane protein of Brucella abortus with similarity to PAL lipoprotein. Infect. Immun.. 62, 3633-3639.
31. Vinals.C, Depiereux.E. and Feytmans.E. (1993) Prediction of structurally conserved regions of D-specific hydroxy acid dehydrogenases by multiple alignment with formate dehydrogenase. Biochem. Biophys. Res. Commun.. 192. 182-188.
32. Vinals.C.. De Bolle.X.. Depiereux.E. and Feytmans.E. (1995) Knowledge-based modelling of the D-lactate dehydrogenase three-dimensional structure. Protein Struct Fund. Genet., 21, 307-318.
33. Vingron.M. and Argos.P. (1991) Motif recognition and alignment for many sequences by comparison of dot-matrices. J. Mol. Bioi, 218, 33-43.
34. Waterman and Jones (1990) Consensus methods for DNA and protein sequence alignment. Methods Enzymoi, 183. 567-577.