Association algorithm to mine the rules that govern enzyme definition and to classify protein sequences

BMC Bioinformatics

Volumn 7, Issue , 2006, Pages

  Chiu, Shih Hau ^a,b   Chen, Chien Chi ^a   Yuan, Gwo Fang ^a   Lin, Thy Hou ^b  

^a FOOD INDUSTRY RESEARCH AND DEVELOPMENT INSTITUTE   (Taiwan)

^b NATIONAL TSING HUA UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

ASSOCIATION ALGORITHMS; AUTOMATIC ANNOTATION; ENZYME CLASSIFICATION; FUNCTIONAL ANNOTATION; GENOME PROJECTS; MANUAL ANNOTATION; PROTEIN SEQUENCES; TRAINING DATASET;

ALGORITHMS; DATA PROCESSING; PROTEINS;

ENZYMES;

ENZYME; FUNGAL PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; CLASSIFICATION; CONTROLLED STUDY; EMBL NUCLEOTIDE SEQUENCE DATABASE; FUNGAL GENE; KNOWLEDGE BASE; NONHUMAN; PROKARYOTE; SWISS-PROT; UNIPROT; CHEMISTRY; DATA BASE; INFORMATION RETRIEVAL; PROCEDURES; PROTEIN DATABASE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

EUKARYOTA; FUNGI; PROKARYOTA;

ALGORITHMS; DATABASE MANAGEMENT SYSTEMS; DATABASES, PROTEIN; ENZYMES; FUNGAL PROTEINS; INFORMATION STORAGE AND RETRIEVAL; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN;

EID: 33747700876     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-304     Document Type: Article

References (15)

1. Gattiker A, Michoud K, Rivoire C, Auchincloss AH, Coudert E, Lima T, Kersey P, Pagni M, Sigrist CJ, Lachaize C, Veuthey AL, Gasteiger E, Bairoch A: Automated annotation of microbial proteomes in SWISS-PROT. Comput Biol Chem 2003, 27(1):49-58.
2. Andrade MA, Brown NP, Leroy C, Hoersch S, de Daruvar A, Reich C, Franchini A, Tamames J, Valencia A, Ouzounis C, Sander C: Automated genome sequence analysis and annotation. Bioinformatics 1999, 15(5):391-412.
3. Biswas M, O'Rourke JF, Camon E, Fraser G, Kanapin A, Karavidopoulou Y, Kersey P, Kriventseva E, Mittard V, Mulder N, Phan I, Servant F, Apweiler R: Applications of InterPro in protein annotation and genome analysis. Brief Bioinform 2002, 3(3):285-295.
4. Holm L, Sander C: Parser for Protein-Folding Units. Proteins 1994, 19(3):256-268.
5. Nagarajan N, Yona G: Automatic prediction of protein domains from sequence information using a hybrid learning system. Bioinformatics 2004, 20(9):1335-1360.
6. Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, Bucher P, Cerutti L, Corpet F, Croning MD, Durbin R, Falquet L, Fleischmann W, Gouzy J, Hermjakob H, Hulo N, Jonassen I, Kahn D, Kanapin A, Karavidopoulou Y, Lopez R, Marx B, Mulder NJ, Oinn TM, Pagni M, Servant F, Sigrist CJ, Zdobnov EM: The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res 2001, 29(1):37-40.
7. Kretschmann E, Fleischmann W, Apweiler R: Automatic rule generation for protein annotation with the C4.5 data mining algorithm applied on SWISS-PROT. Bioinformatics 2001, 17(10):920-926.
8. Bazzan ALC, Engel PM, Schroeder LF, da Silva SC: Automated annotation of keywords for proteins related to mycoplasmataceae using machine learning techniques. Bioinformatics 2002, 18:S35-S43.
9. Creighton C, Hanash S: Mining gene expression databases for association rules. Bioinformatics 2003, 19(1):79-86.
10. Doddi S, Marathe A, Ravi SS, Torney DC: Discovery of association rules in medical data. Med Inform Internet Med 2001, 26(1):25-33.
11. Yang S, Doolittle RF, Bourne PE: Phylogeny determined by protein domain content. PNAS 2005, 102(2):373-378.
12. Phan IQ, Pilbout SF, Fleischmann W, Bairoch A: NEWT, a new taxonomy portal. Nucleic Acids Res 2003, 31(13):3822-3823.
13. Witten JH, Frank E: Data Mining: Practical machine learning tools and techniques. 2nd edition. San Francisco: Morgan Kaufmann; 2005.
14. Agrawal R, Imielinski T, Swami A: Mining Association Rules between Sets of Items in Large Databases. Proc of the ACM SIGMOD Conference: 1993 1993:207-216.
15. Agrawal R, Srikant R: Fast Algorithms for Mining Association Rules. Proc of the 20th VLDB Conference: 1994 1994:487-499.