Efficient discovery of conserved patterns using a pattern graph

Bioinformatics

Volumn 13, Issue 5, 1997, Pages 509-522

  Jonassen, Inge ^a  

^a UNIVERSITY OF BERGEN   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; COMPUTER PROGRAM; DATA BASE; GENETIC PROCEDURES; PATTERN RECOGNITION; PRIORITY JOURNAL; SCORING SYSTEM;

ALGORITHMS; AMINO ACID SEQUENCE; COMPUTER COMMUNICATION NETWORKS; DATABASES, FACTUAL; DECISION TREES; INFORMATION STORAGE AND RETRIEVAL; PATTERN RECOGNITION, AUTOMATED; TERMINOLOGY;

EID: 0030670589     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/13.5.509     Document Type: Article

References (16)

1. Angluin.D. (1980) Finding patterns common to a set of strings. J. Comp Syst. 5c/.. 21, 46-62.
2. Bairoch.A. and Boeckmann.B. (1994) The SWISS-PROT protein sequence data bank: current status. Nucleic Acids Res., 22, 3578-3580.
3. Bairoch.A.. Bucher.P. and Hofman.K. (1995) The PROSITE database, its status in 1995. Nucleic Acids Res.. 24. 189-196.
4. Brazma.A., Jonassen, I., Eidhammer, I. and Gilbert, D.R. (1995) Approaches to the Automatic Discovery of Patterns in Biosequences. Reports in Informatics 113. Department of Informatics, University of Bergen.
5. Etzold.T. and Argos, P. (1993) SRS—an indexing and retrieval tool for flat file data libraries. Comput. Apphc Biosci., 9, 49-57.
6. Jonassen, I., CollinsJ.F. and Higgins, D.G. (1995) Finding flexible patterns in unaligned protein sequences. Protein 5c/., 4, 1587-1595.
7. Lathrop.R., Webster.T, Smith, R., Winston.P. and Smith.T. (1993) Integrating AI with sequence analysis. In Hunter, L. (ed.), Artificial Intelligence and Molecular Biology. AAA1 Press/The MIT Press, pp. 211-258.
8. Neuwald.A.F. and Green, P. (1994) Detecting patterns in protein sequences. J. Mol Biol., 239, 689-712.
9. Roytberg.M.A. (1992) A search for common patterns in many sequences. Comput. Apphc. Biosci., 8, 7-64.
10. Smith.H.O.. Annau.T.M. and Chandrasegaran.S. (1990) Finding sequence motifs in groups of functionally related proteins. Proc. NatlAcad Sa. USA, 87, 826-830.
11. Smith, R.F. and Smith.T.F. (1990) Automatic generation of primary sequence patterns from sets of related protein sequences. Proc Nail Acad.Sa. USA, 87, 118-122.
12. Staden.R. (1989) Methods for discovering novel motifs in nucleic acid sequences. Comput. Applic. Biosci., 5, 293—298.
13. Sturrock.S.S. and CollinsJ.F. (1993) MPsrch version 1.3J. Technical report, Biocomputing Research Unit, University of Edinburgh, UK.
14. Tatusov, R.L, Altschul, S.F. and Koonin.E.V. (1994) Detection of conserved segments in proteins: Iterative scanning of sequence databases with alignment blocks. Proc Natl Acad. Sci. USA, 91, 12091-12095.
15. Taylor, W.R., Flores, TP. and Orengo, C.A. (1994) Multiple protein structure alignment. Protein Sci., 3, 341-348.
16. ThompsonJ.D., Higgins.D.G. and Gibson, T.J. (1994) Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673--4680.