Benchmarking homology detection procedures with low complexity filters

Bioinformatics

Volumn 25, Issue 19, 2009, Pages 2500-2505

  Forslund, Kristoffer ^a   Sonnhammer, Erik L L ^a  

^a STOCKHOLM UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

MEMBRANE PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; DIGITAL FILTERING; FALSE POSITIVE RESULT; INFORMATION PROCESSING; PRIORITY JOURNAL; PROTEOMICS; QUALITY CONTROL; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE DATABASE; SEQUENCE HOMOLOGY; SPECIES COMPARISON;

AMINO ACID SEQUENCE; BENCHMARKING; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 70349850981     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp446     Document Type: Article

References (25)

1. Altschul,S.F. et al. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
2. 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.
3. Altschul,S.F. et al. (2005) Protein database searches using compositionally adjusted substitution matrices. FEBS J., 272 5101-5109
4. Berglund,A.C. et al. (2008) InParanoid 6: Eukaryotic ortholog clusters with inparalogs. Nucleic Acids Res., 36, D263-D266.
5. Chandonia,J.M. et al. (2004) The ASTRAL compendium in 2004. Nucleic Acids Res., 32, D189-D192.
6. Durbin,R. et al. (1998). Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press, Cambridge, UK.
7. Eddy,S.R. (2008) A probabilistic model of local sequence alignment that simplifies statistical significance estimation. PLoS Comput. Biol. 4, e1000069.
8. Eichinger,L. (2005) The genome of the social amoeba Dictyostelium discoideum. Nature, 435, 43-57.
9. Finn,R.D. et al. (2006) Pfam: Clans, web tools and services. Nucleic Acids Res., 34, D247-D251.
10. Finn,R.D. et al. (2008) The Pfam protein families database. Nucleic Acids Res., 36, D281-D288.
11. Forslund,K. et al. (2008) Domain tree-based analysis of protein architecture evolution. Mol. Biol. Evol., 25,254-264.
12. Gough,J. (2005) Convergent evolution of domain architectures (is rare). Bioinformatics, 21, 1464-1471.
13. Gough,J. et al. (2001) Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. J. Mol. Biol., 313, 903-919.
14. Krogh,A. et al. (1994). Hidden Markov models in computational biology. Applications to protein modeling. J. Mol. Biol., 235 1501-1531.
15. Madera,M. and Gough,J. (2002) A comparison of profile hidden Markov model procedures for remote homology detection. Nucleic Acids Res. 30, 4321-4328.
16. 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.
17. Remm,M. et al. (2001) Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J. Mol. Biol., 314, 1041-1052.
18. Schäffer,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.
19. Sonnhammer,E.L. and Durbin,R. (1994) An expert system for processing sequence homology data. ISMB, 2, 363-368.
20. Sonnhammer,E.L. et al. (1998) Pfam: Multiple sequence alignments and HMM-profiles of protein domains. Nucleic Acids Res., 26, 320-322.
21. Wistrand,M. and Sonnhammer,E.L. (2005) Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER. BMC Bioinformatics, 6, 99.
22. Wootton,J.C. and Federhen,S. (1996) Analysis of compositionally biased regions in sequence databases. Methods Enzymol., 266, 554-571.
23. Yu,Y.K. and Altschul,S.F. (2005) The construction of amino acid substitution matrices for the comparison of proteins with non-standard compositions. Bioinformatics, 21, 902-911.
24. Yu,Y.K. et al. (2003) The compositional adjustment of amino acid substitution matrices. Proc. Natl. Acad. Sci. U S A, 100, 15688-15693.
25. Yu,Y.K. et al. (2006) Retrieval accuracy, statistical significance and compositional similarity in protein sequence database searches. Nucleic Acids Res., 34, 5966-5973.