Comparison study on k-word statistical measures for protein: From sequence to 'sequence space'

BMC Bioinformatics

Volumn 9, Issue , 2008, Pages

  Dai, Qi ^a   Wang, Tianming ^a  

^a DALIAN UNIVERSITY OF TECHNOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

CLASSIFICATION TASKS; EVOLUTIONARY INFORMATION; EXPERIMENTAL ASSESSMENT; GENERALIZED RELATIVE ENTROPIES; PHYLOGENETIC ANALYSIS; PROTEIN STRUCTURES; RECEIVER OPERATING CURVES; STATISTICAL MEASURES;

ALIGNMENT; EXPERIMENTS; PROTEINS;

STATISTICS;

PROTEIN;

ACCURACY; AMINO ACID SEQUENCE; AREA UNDER THE CURVE; ARTICLE; CLASSIFICATION; COMPARATIVE STUDY; CONTROLLED STUDY; PHYLOGENY; QUANTITATIVE ANALYSIS; RECEIVER OPERATING CHARACTERISTIC; SENSITIVITY AND SPECIFICITY; STATISTICAL ANALYSIS; ALGORITHM; CHEMICAL MODEL; CHEMISTRY; COMPUTER PROGRAM; COMPUTER SIMULATION; METHODOLOGY; MOLECULAR GENETICS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; STATISTICAL MODEL;

ALGORITHMS; AMINO ACID SEQUENCE; COMPUTER SIMULATION; DATA INTERPRETATION, STATISTICAL; MODELS, CHEMICAL; MODELS, STATISTICAL; MOLECULAR SEQUENCE DATA; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE HOMOLOGY, AMINO ACID; SOFTWARE;

EID: 54149091987     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-394     Document Type: Article

References (48)

1. Bateman A Birney E Cerruti L Durbin R Etwiller L Eddy SR Griffiths JS Howe KL Marshall M Sonnhammer ELL The Pfam Protein FamiliesDatabase Nucleic Acids Res 2002, 30:276-280. 99071 11752314
2. Andreeva A Howorth D Brenner SE Hubbard TJP Chothia C Murzin AG SCOP database in refinements integrate structure and sequence family data Nucleic Acid Res 2004, 32:D226-D229. 308773 14681400
3. Bairoch A Apweiler R The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000 Nucleic Acids Res 2000, 28:45-48. 102476 10592178
4. Wu CH Huang H Arminski L Castro-Alvear J Chen Y Hu ZZ Ledley RS Lewis KG Mewes HW Orcutt BC Suzek BE Tsugita A Vinayaka CR Yeh LSL Zhang J Barker WC The Protein Information Resource, an integrated public resource of functional annotation of proteins Nucleic Acids Res 2002, 30:35-37. 99125 11752247
5. Altschul SF Gish W Miller W Myers EW Lipman DJ Basic local alignment search tool J Mol Biol 1990, 215:403-410. 2231712
6. 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, 25:3389-3402. 146917 9254694
7. Pham TD Spectral distortion measures for biological sequence comparisons and database searching Pattern Recog 2007, 40:516-529.
8. Felsenstein J Evolutionary trees from DNA sequences, a maximum likelihood approach J Mol Evol 1981, 17:368-376. 7288891
9. Felsenstein J Inferring phylogenies from protein sequences by parsimony, distance and likelihood methods Meth Enzymol 1996, 266:418-427. 8743697
10. Huelsenbeck JP Ronquist F MRBAYES: Bayesian inference of phylogenetic trees Bioinformatics 2001, 17:754-755. 11524383
11. Kumar S Tamura K Nei M MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment Brief Bioinform 2004, 5(2):150-163. 15260895
12. Ronquist F Huelsenbeck JP MrBayes 3: Bayesian phylogenetic inference under mixed models Bioinformatics 2003, 19:1572-1574. 12912839
13. Komatsu K Zhu S Fushimi H Qui TK Cai S Kadota S Phylogenetic analysis based on 18S rRNA gene and matK gene sequences of Panax vietnamensis and five related species Planta Med 2001, 67:461-465. 11488463
14. Vinga S Gouveia-Oliveira R Almeida JS Comparative evaluation of word composition distances for the recognition of SCOP relationships Bioinformatics 2004, 20(2):206-15. 14734312
15. Ferragina P Giancarlo R Greco V Manzini G Valiente G Compression-based classification of biological sequences and structures via the Universal Similarity Metric: Experimental assessment BMC Bioinformatics 2007, 8:252-272. 1939857 17629909
16. Vinga S Almeida J Alignment-free sequence comparison - a review Bioinformatics 2003, 19:513-523. 12611807
17. Pham TD Zuegg J A probabilistic measure for alignment-free sequence comparison Bioinformatics 2004, 20:3455-3461. 15271780
18. Blaisdell BE A measure of the similarity of sets of sequences not requiring sequence alignmen Proc Natl Acad Sci USA 1986, 83:5155-5159. 323909 3460087
19. Wu TJ Burke JP Davison DB A measure of DNA sequence dissimilarity based on Mahalanobis distance between frequencies of words Biometrics 1997, 53:1431-1439. 9423258
20. Wu TJ Hsieh YC Li LA Statistical measures of DNA dissimilarity under Markov chain models of base composition Biometrics 2001, 57:441-448. 11414568
21. Stuart GW Moffett K Baker S Integrated gene and species phylogenies from unaligned whole genome protein sequences Bioinformatics 2002, 18:100-108. 11836217
22. Fichant G Gautier C Statistical method for predicting protein coding regions in nucleic acid sequences Comput Appl Biosci 1987, 3:287-295. 3134115
23. Wu KP Lin HN Sung TY Hsu WL A New Similarity Measure among Protein Sequences Proceedings of IEEE CSB2003 Computer Society Bioinformatics Conference 2003, 347-352.
24. Didier G Laprevotte I Pupin M Hénaut A Local decoding of sequences and alignment-free comparison J Comput Biol 2006, 13:1465-1476. 17061922
25. Kelil A Wang S Brzezinski R Fleury A CLUSS: Clustering of Protein Sequences Based on a New Similarity Measure BMC Bioinformatics 2007, 8:286-305. 1976428 17683581
26. Hochreiter S Heusel M Obermayer K Fast model-based protein homology detection without alignment Bioinformatics 2007, 23:1728-1736. 17488755
27. Chew LP Kedem K Finding the Consensus Shape for a Protein Family Algorithmica 2003, 38:115-129.
28. Sierk M Person W Sensitivity and Selectivity in Protein Structure Comparison Protein Sci 2004, 13(3):773-785. 2286722 14978311
29. Thiruv B Quon G Saldanha SA Steipe B Nh3D: A Reference Dataset of Non-Homologous Protein Structures BMC Struct Biol 2005, 5:12. 1182382 16011803
30. Word JM Lovell SC LaBean TH Taylor HC Zalis ME Presley BK Richardson JS Richardson DC Visualizing and Quantifying Molecular Goodness-of-Fit: Small-Probe Contact Dots with Explicit Hydrogen Atoms J Mol Biol 1999, 285(4):1711-1733. 9917407
31. Krasnogor N Pelta DA Measuring the Similarity of Protein Structures by Means of the Universal Similarity Metric Bioinformatics 2004, 20(7):1015-1021. 14751983
32. Rost B Sander C Prediction of protein secondary structure at better than 70% accuracy J Mol Biol 1993, 232:584-599. 8345525
33. Barthel D Hirst JD Blazewicz J Burke EK Krasnogor N ProCKSI: A Decision Support System for Protein (Structure) Comparison, Knowledge, Similarity and Information BMC Bioinformatics 2007, 8:416. 2222653 17963510
34. SCOP: Structural Classification of Proteins http://scop.mrclmb.cam.ac.uk/scop
35. Pearl F et al.: The CATH Domain Structure Database and Related Resources Gene3D and DHS Provide Comprehensive Domain Family Information for Genome Analysis Nucleic Acids Res 2005, 33(D):D247-D251. 539978 15608188
36. Li W Godzik A Cd-hit A fast program for clustering and comparing large sets of protein or nucleotide sequences Bioinformatics 2006, 22:1658-1659. 16731699
37. Felsenstein J PHYLIP-Phylogeny inference package (version 3.2) Cladistics 1989, 5:164-166.
38. Saitoh N Goldberg I Earnshaw WC The SMC proteins and the coming of age of the chromosome scaffold hypothesis BioEssays 1995, 17:759-766. 8763828
39. Lowe J Cordell SC Ent Van Den F Crystal structure of the SMC head domain: An ABC ATPase with 900 residues antiparallel coiled-coil inserted J Mol Biol 2001, 306:25-35. 11178891
40. Hirano M Hirano T Hinge-mediated dimerization of SMC protein is essential for its dynamic interaction with DNA EMBO J 2002, 21:5733-5744. 131072 12411491
41. Cobbe N Heck MM SMCs in the world of chromosome biology- from prokaryotes to higher eukaryotes J Struct Biol 2000, 129:123-143. 10806064
42. Soppa J Prokaryotic structural maintenance of chromosomes (SMC) proteins: Distribution, phylogeny, and comparison with MukBs and additional prokaryotic and eukaryotic coiled-coil proteins Gene 2001, 278:253-264. 11707343
43. Taylor EM Moghraby JS Lees JH Smit B Moens PB Lehmann AR Characterization of a novel human SMC heterodimer homologous to the Schizosaccharomyces pombe Rad18/Spr18 complex Mol Biol Cell 2001, 12:1583-1594. 37326 11408570
44. Fujioka Y Kimata Y Nomaguchi K Watanabe K Kohno K Identification of a novel non-SMC component of the SMC5/SMC6 complex involved in DNA repair J Biol Chem 2002, 277:21585-21591. 11927594
45. Reinert G Schbath S Waterman MS Probabilistic and statistical properties of words: An overview J Comput Biol 2000, 7:1-46. 10890386
46. Kroupa T Measure of divergence of possibility measures Proceedings of the 6th Workshop on Uncertainty Processing (WUPES'2003), Hejnice, Czech Republic 173-181.
47. Egan JP Signal Detection Theory and ROC-Analysis Academic Press, New York 1975.
48. Bradley AP The use of the area under the ROC curve in the evaluation of machine learning algorithms Pattern Recog 1997, 30:1145-1159.