Relation between weight matrix and substitution matrix: Motif search by similarity

Bioinformatics

Volumn 21, Issue 7, 2005, Pages 938-943

  Zheng, Wei Mou ^a  

^a INSTITUTE OF THEORETICAL PHYSICS   (China)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; HELIX LOOP HELIX PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; COMPARATIVE STUDY; MOLECULAR MODEL; PRIORITY JOURNAL; PROBABILITY; PROTEIN MOTIF; SCORING SYSTEM; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; STATISTICAL SIGNIFICANCE;

EID: 16344382055     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti090     Document Type: Article

References (11)

1. Bailey,T. and Elkan,C. (1995) Unsupervised learning of multiple motifs in biopolymers using expectation maximization. Machine Learning, 21, 51-80.
2. Boguski,M.S., Ostell, J. and States,D.J. (1992) Protein engineering: a practical approach. In: Ries,A.R., Sternberg,M.J.E. and Wetzel,R. (eds), IRL Press, Oxford, pp.57-88.
3. Conlon,E.M., Liu,X.S., Lieb,J.D. and Liu,J.S. (2003) Integrating regulatory motif discovery and genome-wide expression analysis. Proc. Natl Acad. Sci., USA, 100, 3339-3344.
4. Eddy,S. (1995) Multiple alignment using hidden Markov models. In Proceedings of the International Conference on Intelligent Systems for Molecular Biology, Cambridge, UK, July 16-19. AAAI/MIT Press, Cambridge, pp. 114-120.
5. Hastings,W.K. (1970) Monte Carlo sampling methods using Markov chains and their applications. Biometrika, 57, 97-109.
6. Helden,J.V., Andre,B. and Collado-Vides,J. (1998) Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J. Mol. Biol., 281, 827-842.
7. Henikoff,S. and Henikoff,J.G. (1992) Amino acid substitution matrices from protein blocks. Proc. Natl Acad. Sci., USA, 89, 10915-10919.
8. Hertz,G., Hartzell,G.,III and Stormo,G. (1990) Identification of consensus patterns in unaligned dna sequences known to be functionally related. Comput. Appl. Biosci., 6, 81-92.
9. Hughey,R. and Krogh,A. (1996) Hidden Markov models for sequence analysis: extension and analysis of the basic method. Comput. Appl. Biosci., 12, 95-107.
10. Lawrence,C.E., Altshul,S., Boguski,M., Liu,J., Neuwald,A. and Wootton,J. (1993) Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignments. Science, 262, 208-214.
11. Thompson,W., Rouchka,E.C. and Lawrence,C.E. (2003) Gibbs recursive sampler: finding transcription factor binding sites. Nucleic Acids Res., 31, 3580-3585.