Use of multiple profiles corresponding to a sequence alignment enables effective detection of remote homologues

Bioinformatics

Volumn 21, Issue 12, 2005, Pages 2821-2826

  Anand, B ^a,b   Gowri, V S ^a   Srinivasan, N ^a  

^a INDIAN INSTITUTE OF SCIENCE   (India)

^b INDIAN INSTITUTE OF TECHNOLOGY KANPUR   (India)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTICAL ERROR; ARTICLE; COMPARATIVE STUDY; COMPUTER MODEL; COMPUTER PROGRAM; INFORMATION PROCESSING; INFORMATION RETRIEVAL; MATHEMATICAL COMPUTING; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN STRUCTURE; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY;

EID: 20844438512     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti432     Document Type: Article

References (17)

1. Altschul,S.F. et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
2. Balaji,S. et al. (2001) PALI - a database of Phylogeny and ALIgnment of homologous protein structures. Nucleic Acids Res., 29, 61-65.
3. Baldi,P. et al. (1994) Hidden Markov models of biological primary sequence information. Proc. Natl Acad. Sci., 91, 1059-1063.
4. Bateman,A. et al. (2002) The Pfam protein families database. Nucleic Acids Res., 30, 276-280.
5. Eddy,S.R. (1998) Profile hidden Markov models. Bioinformatics, 14, 755-763.
6. Evans,S.V. (1993) SETOR: hardware lighted three-dimensional solid model representations of macromolecules. J. Mol. Graph, 11, 134-138.
7. Gowri,V.S. et al. (2003) Integration of related sequences with protein three-dimensional structural families in an updated version of PALI database. Nucleic Acids Res., 31, 486-488.
8. Gribskov,M. et al. (1987) Profile analysis: detection of distantly related proteins. Proc. Natl Acad. Sci., 84, 4355-4358.
9. Karplus,K. et al. (1998) Hidden Markov models for detecting remote protein homologies. Bioinformatics, 14, 846-856.
10. Krogh,A. et al. (1994) Hidden Markov models in computational biology. Applications to protein modelling. J. Mol. Biol., 235, 1501-1531.
11. Lindahl,E. and Elofsson,A. (2000) Identification of related proteins on family, superfamily and fold level. J. Mol. Biol., 295, 613-625.
12. Muller,A. et al. (1999) Benchmarking PSI-BLAST in genome annotation. J. Mol. Biol., 293, 1257-1271.
13. Murzin,A.G. et al. (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
14. Park,J. et al. (1998) Sequence comparisons using multiple sequences detect three times as many remote homologues as pair-wise methods. J. Mol. Biol., 284, 1201-1210.
15. Pandit,S.B et al. (2004) SUPFAM: a database of sequence superfamilies of protein domains. BMC Bioinform., 5, 28.
16. Schaffer,A.A. et al. (1999) IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices. Bioinformatics, 12, 1000-1011.
17. Sonnhammer,E.L. et al. (1997) Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins, 28, 405-420.