CLUSS: Clustering of protein sequences based on a new similarity measure

BMC Bioinformatics

Volumn 8, Issue , 2007, Pages

  Kelil, Abdellali ^a   Wang, Shengrui ^a   Brzezinski, Ryszard ^a   Fleury, Alain ^a  

^a UNIVERSITÉ DE SHERBROOKE   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL FUNCTIONS; BIOLOGICAL PHENOMENA; EVOLUTIONARY MODELS; EXPERIMENTAL COMPARISON; FUNCTIONAL ACTIVITIES; FUNCTIONAL CHARACTERISTICS; PHYLOGENETIC ANALYSIS; PHYLOGENETIC RELATIONSHIPS;

AMINO ACIDS; BIOLOGICAL SYSTEMS; PROTEINS;

CLUSTERING ALGORITHMS;

ACCURACY; ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; COMPUTER PROGRAM; GENE CLUSTER; INFORMATION PROCESSING; MATHEMATICAL COMPUTING; MOLECULAR PHYLOGENY; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PHYLOGENY; PREDICTION; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN FUNCTION; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; CHEMISTRY; CLUSTER ANALYSIS; DNA SEQUENCE; GENETICS; METHODOLOGY; MOLECULAR EVOLUTION; MOLECULAR GENETICS; MULTIGENE FAMILY;

PROTEIN;

ALGORITHMS; AMINO ACID SEQUENCE; CLUSTER ANALYSIS; EVOLUTION, MOLECULAR; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, AMINO ACID; SOFTWARE;

EID: 34548605214     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-286     Document Type: Article

References (47)

1. Altschul SF Gish W Miller W Myers EW Lipman DJ Basic local alignment search tool J Mol Bio 1990 215 403-410
2. 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 Nucl Acids Res 1997 25 3389-3402 146917 9254694 10.1093/nar/ 25.17.3389
3. Krause A Stoye J Vingron M The SYSTERS protein sequence cluster set Nucl Acids Res 2000 28 270-272 102384 10592244 10.1093/nar/28.1.270
4. Pipenbacher P Schliep A Schneckener S Schonhuth A Schomburg D Schrader R ProClust: Improved clustering of protein sequences with an extended graph-based approach Bioinformatics 2002 18 S182-S191 10.1093/ bioinformatics/18.1.182 12386002
5. Yona G Linial N Linial M ProtoMap: Automatic classification of protein sequences and hierarchy of protein families Nucl Acids Res 2000 28 49-55 102438 10592179 10.1093/nar/28.1.49
6. Sjölander K Phylogenomic inference of protein molecular function: Advances and challenges Bioinformatics 2004 20 170-179 10.1093/ bioinformatics/bth021 14734307
7. Basic Local Alignment Search Tool http://www.ncbi.nlm.nih.gov/BLAST
8. Enright AJ Van Dongen S Ouzounis CA An efficient algorithm for large-scale detection of protein families Nucl Acids Res 2002 30 1575-1584 101833 11917018 10.1093/nar/30.7.1575
9. Tetko IV Facius A Ruepp A Mewes HW Super Paramagnetic Clustering of Protein Sequences BMC Bioinformatics 2005 6 82 1084344 15804359 10.1186/ 1471-2105-6-82
10. Sjölander K Phylogenetic inference in protein superfamilies: Analysis of SH2 domains Intell Syst Mol Biol 1998 6 165-174
11. Wicker N Perrin GR Thierry JC Poch O Secator: A Program for Inferring Protein Subfamilies from Phylogenetic Trees Mol Biol Evol 2001 18 1435-1441 11470834
12. Jothi R Zotenko E Tasneem A Przytycka TM COCO-CL: Hierarchical clustering of homology relations based on evolutionary correlations Bioinformatics 2006 22 779-788 1620014 16434444 10.1093/bioinformatics/ btl009
13. Ward JH Hierarchical Grouping to Optimize an Objective Function J Am Stat Assoc 1963 58 236-244 10.2307/2282967
14. Ward JH Hook ME Application of a Hierarchical Grouping Procedure to a Problem of Grouping Profiles Educ Psychol Meas 1963 23 69-82 10.1177/ 001316446302300107
15. Batagelj V Generalized Ward and related clustering problems Classification and Related Methods of Data Analysis Amsterdam: Elsevier Bock HH 1998 67-74
16. Duda RO Hart PE Stork DG Pattern Classification John Wiley and Sons second 2001
17. Varré JS Delahaye JP Rivals E The transformation distance: A dissimilarity measure based on movements of segments Bioinformatics 1999 15 194-202 10.1093/bioinformatics/15.3.194 10222406
18. Sonnhammer ELL Hollich V Scoredist: A simple and robust sequence distance estimator BMC Bioinformatics 2005 6 108 1131889 15857510 10.1186/1471-2105-6-108
19. Higgins D Multiple alignment The Phylogenetic Handbook Cambridge University Press Salemi M, Vandamme AM 2004 45 45-71
20. Reinert G Schbath S Waterman MS Probabilistic and statistical properties of words: An overview J Comp Biol 2000 7 1-46 10.1089/10665270050081360
21. Rocha J Rossello F Segura J The Universal Similarity Metric does not detect domain similarity Q-bio QM 2006 1 0603007
22. Edgar RC Local homology recognition and distance measures in linear time using compressed amino acid alphabets Nucl Acids Res 2004 32 380-385 373290 14729922 10.1093/nar/gkh180
23. Vinga S Almeida J Alignment-free sequence comparison - A review Bioinformatics 2003 19 513-523 10.1093/bioinformatics/btg005 12611807
24. Kimura M Evolutionary rate at the molecular level Nature 1968 217 624-626 10.1038/217624a0 5637732
25. Felsenstein J An alternating least squares approach to inferring phylogenies from pairwise distances Syst Biol 1997 46 101 10.2307/ 2413638 11975348
26. Henikoff S Henikoff JG Amino acid substitution matrices from protein blocks Proceedings of the National Academy of Sciences of the United States of America 1992 89 10915-10919 50453 1438297 10.1073/ pnas.89.22.10915
27. Dayhoff MO Schwartz RM Orcutt BC A model of evolutionary change in proteins Atlas of Protein Sequence and Structure 1978 5 suppl 3 345-352
28. Karlin S Ost F Maximal length of common words among random letter sequences The Annals of Probability 1988 16 535-563
29. Karlin S Ghandour G Comparative statistics for DNA and protein sequences: Single sequence analysis Proc Natl Acad Sci USA 1985 82 5800-5804 390640 2994049 10.1073/pnas.82.17.5800
30. Karlin S Ghandour G Comparative statistics for DNA and protein sequences: Multiple sequence analysis Proc Natl Acad Sci USA 1985 82 6186-6190 391017 3929250 10.1073/pnas.82.18.6186
31. Phylogenetic classification of proteins encoded in complete genomes http://www.ncbi.nlm.nih.gov/COG/
32. GPCRIPDB: Information system for GPCR interacting proteins http://www.gpcr.org
33. The carbohydrate-active enzymes (CAZy) database http://www.cazy.org/
34. Titgemeyer F Reizer J Reizer A Saier MH Jr Evolutionary relationships between sugar kinases and transcriptional repressors in bacteria Microbiology 1994 140 2349-2354 7952186
35. Heringa J Computational methods for protein secondary structure prediction using multiple sequence alignments Current Protein & Peptide Science 2000 1 273-301 10.2174/1389203003381324 12369910
36. Leung MY Blaisdell BE Burge C Karlin S An Efficient Algorithm for Identifying Matches with Errors in Multiple Long Molecular Sequences J Mol Biol 1991 221 1367-1378 10.1016/0022-2836(91)90938-3 1942056
37. Thompson JD Higgins DG Gibson TJ Improved sensitivity of profile searches through the use of sequence weights and gap excision Comput Appl Biosci 1994 10 19-29 8193951
38. Thompson JD Higgins DG Gibson TJ CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucl Acids Res 1994 22 4673-4680 308517 7984417 10.1093/nar/22.22.4673
39. Lodish H Berk A Matsudaira P Kaiser CA Krieger M Scott MP Zipursky L Darnell J Molecular Cell Biology New York and Basingstoke: W.H. Freeman and Co 5 2004
40. Fanning S Leahy M Sheehan D Nucleotide and deduced amino acid sequences of Rhizobium meliloti 102F34 lacZ gene: Comparison with prokaryotic beta-galactosidases and human beta-glucuronidase Gene 1994 141 91-96 10.1016/0378-1119(94)90133-3 8163182
41. Côté N Fleury A Dumont-Blanchette E Fukamizo T Mitsutomi M Brzezinski R Two exo-β-D-glucosaminidases/exochitosanases from actinomycetes define a new subfamily within family 2 of glycoside hydrolases Biochem J 2006 394 675-686 1383717 16316314 10.1042/BJ20051436
42. Ike M Isami K Tanabe Y Nogawa M Ogasawara W Okada H Morikawa Y Cloning and heterologous expression of the exo-β-D-glucosaminidase-encoding gene (gls93) from a filamentous fungus, Trichoderma reesei PC-3-7 Appl Microbiol Biotechnol 2006 72 687-695 10.1007/s00253-006-0320-y 16636831
43. Ishimizu T Sasaki A Okutani S Maeda M Yamagishi M Hase S Endo-beta-mannosidase, a plant enzyme acting on N-glycan: Purification, molecular cloning and characterization J Biol Chem 2004 279 3855-3862 10.1074/jbc.M406886200
44. Fukamizo T Fleury A Côté N Mitsutomi M Brzezinski R Exo-β-D-glucosaminidase from Amycolatopsis orientalis: Catalytic residues, sugar recognition specificity, kinetics, and synergism Glycobiology 2006 16 1064-1072 10.1093/glycob/cwl026 16877749
45. Edgar RC MUSCLE: A multiple sequence alignment method with reduced time and space complexity BMC Bioinformatics 2004 5 113 517706 15318951 10.1186/1471-2105-5-113
46. Katoh K Misawa K Kuma K Miyata T MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform Nucl Acids Res 2002 30 3059-3066 135756 12136088 10.1093/nar/gkf436
47. Notredame C Higgins D Heringa J T-Coffee: A novel method for multiple sequence alignments Journal of Molecular Biology 2000 302 205-217 10.1006/jmbi.2000.4042 10964570