CORAL: Aligning conserved core regions across domain families

Bioinformatics

Volumn 25, Issue 15, 2009, Pages 1862-1868

  Fong, Jessica H ^a   Marchler Bauer, Aron ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ALGORITHM; ARTICLE; CONTROLLED STUDY; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROCESS OPTIMIZATION; PROTEIN DATABASE; PROTEIN DOMAIN; PROTEIN FAMILY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

ALGORITHMS; AMINO ACID SEQUENCE; CONSERVED SEQUENCE; DATABASES, PROTEIN; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

EID: 67650714435     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp334     Document Type: Article

References (35)

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. Brown,D.P. et al. (2007) Automated protein subfamily identification and classification. PLoS Comput. Biol., 3, e160.
3. Chakrabarti,S. et al. (2006) Refining multiple sequence alignments with conserved core regions. Nucleic Acids Res., 34, 2598-2606.
4. Edgar,R.C. (2004) MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32, 1792-1797.
5. Edgar,R.C. and Sjolander, K. (2004) A comparison of scoring functions for protein sequence profile alignment. Bioinformatics, 20, 1301-1308.
6. Finn,R.D. et al. (2006) Pfam: Clans, web tools and services. Nucleic Acids Res., 34, D247-D251.
7. Gibrat,J.F. et al. (1996) Surprising similarities in structure comparison. Curr. Opin. Struct. Biol., 6, 377-385.
8. Gotoh,O. (1993) Optimal alignment between groups of sequences and its application to multiple sequence alignment. Comput. Appl. Biosci., 9, 361-370.
9. Heger,A. and Holm,L. (2001) Picasso: Generating a covering set of protein family profiles. Bioinformatics, 17, 272-279.
10. Henikoff,J.G. et al. (2000) Increased coverage of protein families with the blocks database servers. Nucleic Acids Res., 28, 228-230.
11. Kann,M.G. et al. (2005) A structure-based method for protein sequence alignment. Bioinformatics, 21, 1451-1456.
12. Kann,M.G. et al. (2007) The identification of complete domains within protein sequences using accurate E-values for semi-global alignment. Nucleic Acids Res., 35, 4678-4685.
13. Karlin,S. and Altschul,S.F. (1990) Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl Acad. Sci. USA, 87, 2264-2268.
14. Kunin,V. et al. (2001) Consistency analysis of similarity between multiple alignments: Prediction of protein function and fold structure from analysis of local sequence motifs. J. Mol. Biol., 307, 939-949.
15. Letunic,I. et al. (2006) SMART 5: Domains in the context of genomes and networks. Nucleic Acids Res., 34, D257-260.
16. Madej,T. et al. (1995) Threading a database of protein cores. Proteins, 23, 356-369.
17. Marchler-Bauer,A. et al. (2002) CDD: A database of conserved domain alignments with links to domain three-dimensional structure. Nucleic Acids Res., 30, 281-283.
18. Marchler-Bauer,A. et al. (2009) CDD: Specific functional annotation with the Conserved Domain Database. Nucleic Acids Res., 37, D205-210.
19. Mittelman,D. et al. (2003) Probabilistic scoring measures for profile-profile comparison yield more accurate short seed alignments. Bioinformatics, 19, 1531-1539.
20. 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.
21. Needleman,S.B. and Wunsch,C.D. (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol., 48, 443-453.
22. Ohlson,T. and Elofsson,A. (2005) ProfNet, a method to derive profile-profile alignment scoring functions that improves the alignments of distantly related proteins. BMC Bioinformatics, 6, 253.
23. Ohlson,T. et al. (2004) Profile-profile methods provide improved fold-recognition: A study of different profile-profile alignment methods. Proteins, 57, 188-197.
24. Panchenko,A.R. (2003) Finding weak similarities between proteins by sequence profile comparison. Nucleic Acids Res., 31, 683-689.
25. Pietrokovski,S. (1996) Searching databases of conserved sequence regions by aligning protein multiple-alignments. Nucleic Acids Res., 24 3836-3845.
26. Rychlewski,L. et al. (2000) Comparison of sequence profiles. Strategies for structural predictions using sequence information. Protein Sci., 9, 232-241.
27. Sadreyev,R. and Grishin,N. (2003) COMPASS: A tool for comparison of multiple protein alignments with assessment of statistical significance. J. Mol. Biol., 326, 317-336.
28. Sauder,J.M. et al. (2000) Large-scale comparison of protein sequence alignment algorithms with structure alignments. Proteins, 40, 6-22.
29. Schaffer,A.A. et al. (2001) Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res., 29, 2994-3005.
30. Smith,T.F. and Waterman,M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
31. Soding,J. (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics, 21, 951-960.
32. Van Walle,I. et al. (2005) SABmark-a benchmark for sequence alignment that covers the entire known fold space. Bioinformatics, 21, 1267-1268.
33. von Ohsen,N. et al. (2003) Profile-profile alignment: A powerful tool for protein structure prediction. Pac. Symp. Biocomput., 252-263.
34. Wilson,D. et al. (2007) The SUPERFAMILY database in 2007: Families and functions. Nucleic Acids Res., 35, D308-D313.
35. Yona,G. and Levitt,M. (2002) Within the twilight zone: A sensitive profile-profile comparison tool based on information theory. J. Mol. Biol., 315, 1257-1275.