OXBench: A benchmark for evaluation of protein multiple sequence alignment accuracy

BMC Bioinformatics

Volumn 4, Issue , 2003, Pages

  Raghava, G P S ^b,c,d   Searle, Stephen M J ^b   Audley, Patrick C ^a   Barber, Jonathan D ^a   Barton, Geoffrey J ^a,b,c  

^a UNIVERSITY OF DUNDEE   (United Kingdom)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^c UNIVERSITY OF OXFORD   (United Kingdom)

^d INSTITUTE OF MICROBIAL TECHNOLOGY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN; FERREDOXIN;

ACCURACY; AMINO ACID SEQUENCE; ANALYTICAL ERROR; ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; GENETIC ALGORITHM; GENETIC CONSERVATION; INTERMETHOD COMPARISON; INTERNET; MATHEMATICAL COMPUTING; PREDICTION; PROTEIN FAMILY; PROTEIN FUNCTION; PROTEIN STRUCTURE; SCORING SYSTEM; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE DATABASE; STATISTICAL SIGNIFICANCE; BIOLOGY; CHEMISTRY; CLUSTER ANALYSIS; COMPARATIVE STUDY; COMPUTER GRAPHICS; EVALUATION STUDY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PROCEDURES; PROTEIN DATABASE; QUALITY CONTROL; REPRODUCIBILITY; SEQUENCE HOMOLOGY; STANDARDS; STATISTICAL DISTRIBUTION; STATISTICS AND NUMERICAL DATA;

SUGARCANE RAMU STUNT DISEASE PHYTOPLASMA;

AMINO ACID SEQUENCE; BENCHMARKING; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; COMPUTER GRAPHICS; CONSERVED SEQUENCE; DATABASES, PROTEIN; FERREDOXINS; INTERNET; MOLECULAR SEQUENCE DATA; PROTEINS; REPRODUCIBILITY OF RESULTS; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; SOFTWARE; SOFTWARE DESIGN; SOFTWARE VALIDATION; STATISTICAL DISTRIBUTIONS;

EID: 2942517966     PISSN: 14712105     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2105-4-47     Document Type: Article

References (54)

1. Taylor WR: Identification of protein sequence homology by consensus template alignment. J Mol Biol 1986, 188:233-258.
2. Barton GJ: Protein sequence alignment and database scanning. In Protein structure prediction: A practical approach Edited by: Sternberg MJE. Oxford: IRL Press at Oxford University Press; 1996:31-63.
3. Livingstone CD and Barton GJ: Protein sequence alignments: a strategy for the hierarchical analysis of residue conservation. Comput Appl Biosci 1993, 9:745-756.
4. Marti-Renom MA, Stuart AC, Fiser A, Sanchez R, Melo F and Sali A: Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct 2000, 29:291-325.
5. Barton GJ and Sternberg MJ: Evaluation and improvements in the automatic alignment of protein sequences. Protein Eng 1987, 1:89-94.
6. Feng DF and Doolittle RF: Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J Mol Evol 1987, 25:351-360.
7. Lipman DJ, Altschul SF and Kececioglu JD: A tool for multiple sequence alignment. Proc Natl Acad Sci USA 1989, 86:4412-4415.
8. Thompson JD, Higgins DG and Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22:4673-4680.
9. Notredame C, Higgins DG and Heringa J: T-coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol 2000, 302:205-17.
10. Needleman SB and Wunsch CD: A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 1970, 48:443-453.
11. Sellers PH: On the theory and computation of evolutionary distances. J App Math 1974, 26:787-793.
12. Murata M, Richardson JS and Sussman JL: Simultaneous comparison of three protein sequences. Proc Natl Acad Sci USA 1985, 82:3073-3077.
13. Barton GJ: Protein multiple sequence alignment and flexible pattern matching. Methods Enzymol 1990, 183:403-28.
14. Barton GJ and Sternberg MJ: A strategy for the rapid multiple alignment of protein sequences, confidence levels from tertiary structure comparisons. J Mol Biol 1987, 198:327-337.
15. Karplus K and Hu B: Evaluation of protein multiple alignments by SAM-T99 using the BAliBASE multiple alignment test set. Bioinformatics 2001, 17:713-20.
16. McClure M, Vasi T and Fitch W: Comparative analysis of multiple protein-sequence alignment methods. Mol Biol Evol 1994, 11:571-592.
17. Gotoh O: Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments. J Mol Biol 1996, 264:823-838.
18. Gotoh O: Optimal alignment between groups of sequences and its application to multiple sequence alignment. Comp App Biosci 1993, 9:361-370.
19. Gotoh O: Further improvement in methods of group-to-group sequence alignment with generalized profile operations. Comp App Biosci 1993, 10:379-387.
20. Gotoh O: A weighting system and algorithm for aligning many phylogenetically related sequences. Comp App Biosci 1995, 11:543-551.
21. Sali A and Overington JP: Derivation of rules for comparative protein modeling from a database of protein structure alignments. Protien Sci 1994, 3:1582-1596.
22. Thompson J, Plewniak F and Poch O: BAliBASE: a benchmark alignment database for the evaluation of multiple sequence alignment programs. Bioinformatics 1999, 15:87-88.
23. Dengler U, Siddiqui AS and Barton GJ: Protein structural domains: analysis of the 3Dee domains database. Proteins 2001, 42:332-344.
24. Siddiqui AS, Dengler U and Barton GJ: 3Dee: a database of protein structural domains. Bioinformatics 2001, 17:200-201.
25. Russell RB and Barton GJ: Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels. Proteins 1992, 14:309-323.
26. Kabsch W and Sander C: Dictionary of protein secondary structure: pattern recognition of hydrogne-bonded and geometrical features. Biopolymers 1983, 22:2577-2637.
27. Laskowski RA, Mac Arthur MW, Moss DS and Thornton JM: PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Cryst 1993, 26:283-291.
28. Godzik A: The structural alignment between two protein: Is there a unique answer? Protien Sci 1996, 5:1325-1338.
29. Feng ZK and Sippl MJ: Optimum superimposition of protein structures: ambiguities and implications. Fold Des 1996, 1:123-132.
30. Barton G: OC - A cluster analysis program. 1993 [http://www.compbio.dundee.ac.uk/Software/OC/oc.html].
31. Hermjakob H, Lang F and Apweiler R: SPTR - A comprehensive, non-redundant and up-to-date view of the protein sequence world. CCP11 Newsletter 1998, 2:.
32. Bairoch A and Boeckmann B: The SWISS-PROT protein sequence data bank. Nucleic Acids Res 1991, 19 Suppl:2247-2249.
33. Morgenstern B, Dress A and Werner T: Multiple DNA and protein sequence alignment based on segment-to-segment comparison. Proc Natl Acad Sci USA 1996, 93:12098-12103.
34. Moult J, Hubbard T, Bryant SH, Fidelis K and Pedersen JT: Critical assessment of methods of protein structure prediction (CASP): round II. Proteins 1997, Suppl 1:2-6.
35. Mclachlan AD: A mathematical procedure for superimposing atomic coordinates of proteins. Acta Crystallogr A 1972, A28:656-657.
36. Diamond R: On the comparison of conformations using linear and quadratic transformations. Acta Crystallogr A 1976, A32:1-10.
37. Rossmann MG, Liljas A, Branden CI and Banaszak LJ: Evolutionary and structural relationships among the dehydrogenases. The Enzymes 1975, 11:61-102.
38. Vogt G, Etzold T and Argos P: An assessment of amino acid exchange matrices in aligning protein sequences: The twilight zone revisited. J Mol Biol 1995, 249:816-831.
39. Ihaka R and Gentleman R: R: A language for data analysis and graphics. Journal of Computational and Graphical Statistics 1996, 5:299-314.
40. Dayhoff MO, Schwartz RM and Orcutt BC: A model of evolutionary change in proteins. Matrices for detecting distant relationships. In Atlas of protein sequence and structure Volume 5. Edited by: Dayhoff MO. Washington DC: National biomedical research foundation; 1978:345-358.
41. Barton GJ: ALSCRIPT: a tool to format multiple sequence alignments. Protein Eng 1993, 6:37-40.
42. Henikoff S and Henikoff JG: Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 1992, 89:10915-10919.
43. Gonnet GH, Cohen MA and Benner SA: Exhaustive matching of the entire protein sequence database. Science 1992, 256:1443-1445.
44. Webber C and Barton GJ: Estimation of P-values for global alignments of protein sequences. Bioinformatics 2001, 17:1158-67.
45. Gupta SK, Kececioglu J and Schaffer AA: Improving the practical space and time efficiency of the shortest-paths approach to sum-of-pairs multiple sequence alignment. J Comput Biol 1995, 2:459-472.
46. Krogh A, Brown M, Mian IS, Sjolander K and Haussler D: Hidden markov models in computational biology: Applications to protein modelling. J Mol Biol 1994, 235:1501-1531.
47. Smith RF and Smith TF: Automatic generation of primary sequence patterns from sets of related protein sequences. Proc Natl Acad Sci USA 1990, 87:118-122.
48. Smith RF and Smith TF: Pattern-induced multi-sequence alignment (PIMA) algorithm employing secondary structure-dependent gap penalties for use in comparitive protein modelling. Proteins 1992, 5:35-41.
49. Cuff JA and Barton GJ: Evaluation and improvement of multiple sequence methods for protein secondary structure prediction. Proteins 1999, 34:508-519.
50. Cuff JA and Barton GJ: Application of multiple sequence alignment profiles to improve protein secondary structure prediction. Proteins 2000, 40:502-511.
51. Murzin A, Brenner SE, Hubbard T and Chothia C: SCOP: a structural classification of proteins database and the investigation of sequences and structures. J Mol Biol 1995, 247:536-540.
52. Vingron M and Argos P: Determination of reliable regions in protein sequence alignments. Protien Eng 1990, 3:565-569.
53. Holmes I and Durbin R: Dynamic programming alignment accuracy. J Comput Biol 1998, 5:493-504.
54. Cline M, Hughey R and Karplus K: Predicting reliable regions in protein sequence alignments. Bioinformatics 2002, 18:306-314.