Considering scores between unrelated proteins in the search database improves profile comparison

BMC Bioinformatics

Volumn 10, Issue , 2009, Pages

  Sadreyev, Ruslan I ^a   Wang, Yong ^c,d   Grishin, Nick V ^a,b  

^a UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

^b UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

^c The University of Texas Southwestern Medical Center   (United States)

^d BAYLOR COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURATE ESTIMATION; DOMINANT CONTRIBUTIONS; MULTIPLE SEQUENCE ALIGNMENTS; PROFILE SIMILARITIES; REMOTE HOMOLOGY DETECTIONS; STATISTICAL SIGNIFICANCE; STRUCTURAL RELATIONSHIP; STRUCTURE PREDICTION;

CALIBRATION; DATABASE SYSTEMS; PROTEINS;

QUERY PROCESSING;

PROTEIN;

ARTICLE; BIOLOGY; CHEMISTRY; COMPARATIVE STUDY; FACTUAL DATABASE; METHODOLOGY; PROTEIN DATABASE; SEQUENCE ANALYSIS;

COMPUTATIONAL BIOLOGY; DATABASES, FACTUAL; DATABASES, PROTEIN; PROTEINS; SEQUENCE ANALYSIS, PROTEIN;

EID: 73149104157     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-399     Document Type: Article

References (20)

1. Zhang Y, Hubner IA, Arakaki AK, Shakhnovich E, Skolnick J. On the origin and highly likely completeness of single-domain protein structures. Proc Natl Acad Sci USA 2006, 103(8):2605-2610. 10.1073/pnas.0509379103, 1413790, 16478803.
2. Shi S, Pei J, Sadreyev RI, Kinch LN, Majumdar I, Tong J, Cheng H, Kim B, Grishin NV. Analysis of CASP8 targets, predictions and assessment methods. Database: The Journal of Biological Database and Curation 2009,
3. Frenkel-Morgenstern M, Singer A, Bronfeld H, Pietrokovski S. One-Block CYRCA: an automated procedure for identifying multiple-block alignments from single block queries. Nucleic Acids Res 2005, (33 Web Server):W281-283. 10.1093/nar/gki488, 1160248, 15980470.
4. Madera M. Profile Comparer: a program for scoring and aligning profile hidden Markov models. Bioinformatics 2008, 24(22):2630-2631. 10.1093/bioinformatics/btn504, 2579712, 18845584.
5. Pietrokovski S. Searching databases of conserved sequence regions by aligning protein multiple-alignments. Nucleic Acids Res 1996, 24(19):3836-3845. 10.1093/nar/24.19.3836, 146152, 8871566.
6. Rychlewski L, Jaroszewski L, Li W, Godzik A. Comparison of sequence profiles. Strategies for structural predictions using sequence information. Protein Sci 2000, 9(2):232-241. 2144550, 10716175.
7. Sadreyev R, Grishin N. COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance. J Mol Biol 2003, 326(1):317-336. 10.1016/S0022-2836(02)01371-2, 12547212.
8. Sadreyev RI, Tang M, Kim BH, Grishin NV. COMPASS server for homology detection: improved statistical accuracy, speed and functionality. Nucleic Acids Res 2009, (37 Web Server):W90-94. 10.1093/nar/gkp360, 2703893, 19435884.
9. Soding J. Protein homology detection by HMM-HMM comparison. Bioinformatics 2005, 21(7):951-960. 10.1093/bioinformatics/bti125, 15531603.
10. Wang Y, Sadreyev RI, Grishin NV. PROCAIN: protein profile comparison with assisting information. Nucleic Acids Res 2009, 25(16):2076-7.
11. Yona G, Levitt M. Within the twilight zone: a sensitive profile-profile comparison tool based on information theory. J Mol Biol 2002, 315(5):1257-1275. 10.1006/jmbi.2001.5293, 11827492.
12. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
13. Frenkel-Morgenstern M, Voet H, Pietrokovski S. Enhanced statistics for local alignment of multiple alignments improves prediction of protein function and structure. Bioinformatics 2005, 21(13):2950-2956. 10.1093/bioinformatics/bti462, 15870168.
14. Sadreyev RI, Grishin NV. Accurate statistical model of comparison between multiple sequence alignments. Nucleic Acids Res 2008, 36(7):2240-2248. 10.1093/nar/gkn065, 2367703, 18285364.
15. Schaffer AA, Aravind L, Madden TL, Shavirin S, Spouge JL, Wolf YI, Koonin EV, Altschul SF. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res 2001, 29(14):2994-3005. 10.1093/nar/29.14.2994, 55814, 11452024.
16. Altschul SF, Wootton JC, Gertz EM, Agarwala R, Morgulis A, Schaffer AA, Yu YK. Protein database searches using compositionally adjusted substitution matrices. Febs J 2005, 272(20):5101-5109. 10.1111/j.1742-4658.2005.04945.x, 1343503, 16218944.
17. Yu YK, Altschul SF. The construction of amino acid substitution matrices for the comparison of proteins with non-standard compositions. Bioinformatics 2005, 21(7):902-911. 10.1093/bioinformatics/bti070, 15509610.
18. Karlin S, Altschul SF. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc Natl Acad Sci USA 1990, 87(6):2264-2268. 10.1073/pnas.87.6.2264, 53667, 2315319.
19. Qi Y, Sadreyev RI, Wang Y, Kim BH, Grishin NV. A comprehensive system for evaluation of remote sequence similarity detection. BMC Bioinformatics 2007, 8:314. 10.1186/1471-2105-8-314, 2031906, 17725841.
20. Jones DT. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 1999, 292(2):195-202. 10.1006/jmbi.1999.3091, 10493868.