SeqHound: Biological sequence and structure database as a platform for bioinformatics research

BMC Bioinformatics

Volumn 3, Issue , 2002, Pages

  Michalickova, Katerina ^a,b   Bader, Gary ^a,b   Dumontier, Michel ^a,b   Lieu, Hao ^b   Betel, Doron ^a,b   Isserlin, Ruth ^a,b   Hogue, Christopher W V ^a,b  

^a UNIVERSITY OF TORONTO   (Canada)

^b MOUNT SINAI HOSPITAL   (Canada)

Author keywords

Local database resource; Sequence database; Structure database

Indexed keywords

ACCESS TO INFORMATION; ARTICLE; BIOINFORMATICS; CLINICAL RESEARCH; COMPUTER INTERFACE; COMPUTER PROGRAM; COST EFFECTIVENESS ANALYSIS; GENBANK; GENE SEQUENCE; GENE STRUCTURE; GENETIC DATABASE; INFORMATION PROCESSING; INFORMATION RETRIEVAL; INFORMATION SYSTEM; INTERNET; LICENCE; MEDICAL RESEARCH; MEDLINE; PROTEIN DOMAIN; PROTEIN FUNCTION; REDUNDANCY ANALYSIS; SCIENTIFIC LITERATURE; SEQUENCE DATABASE; STRUCTURE ACTIVITY RELATION; TAXONOMY; AMINO ACID SEQUENCE; BIOLOGICAL MODEL; BIOLOGY; CHEMICAL STRUCTURE; CLASSIFICATION; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE;

AMINO ACID SEQUENCE; BASE SEQUENCE; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; INFORMATION STORAGE AND RETRIEVAL; INTERNET; MODELS, GENETIC; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; SOFTWARE; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 0012787398     PISSN: 14712105     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2105-3-32     Document Type: Article

References (23)

1. Schuler GD, Epstein JA, Ohkawa H and Kans JA Entrez: molecular biology database and retrieval system. Methods Enzymol 1996, 266:141-162
2. Stoesser G, Baker W, van den BA, Camon E, Garcia-Pastor M, Kanz C, Kulikova T, Leinonen R, Lin Q and Lombard V The EMBL Nucleotide Sequence Database. Nucleic Acids Res 2002, 30:21-26
3. Bader GD and Hogue CW BIND-a data specification for storing and describing biomolecular interactions, molecular complexes and pathways. Bioinformatics 2000, 16:465-477
4. Bader GD, Donaldson I, Wolting C, Ouellette BF, Pawson T and Hogue CW BIND-The biomolecular interaction network database. Nucleic Acids Res 2001, 29:242-245
5. Betel D and Hogue CW Kangaroo - A pattern-matching program for biological sequences. BMC Bioinformatics 2002, 3:20
6. Michalickova K, Dharsee M and Hogue CWV Sequence analysis on a 216 processor Beowulf cluster. 4th Annual Linux Showcase and Conference, Atlanta 2000, 4:111-119
7. Altschul SF, Gish W, Miller W, Myers EW and Lipman DJ Basic local alignment search tool. J Mol Biol 1990, 215:403-410
8. Dumontier M and Hogue CW NBLAST: a cluster variant of BLAST for NxN comparisons. BMC Bioinformatics 2002, 3:13
9. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA and Wheeler DL GenBank. Nucleic Acids Res 2002, 30:17-20
10. Pruitt KD and Maglott DR RefSeq and LocusLink: NCBI genecentered resources. Nucleic Acids Res 2001, 29:137-140
11. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN and Bourne PE The Protein Data Bank. Nucleic Acids Res 2000, 28:235-242
12. Bairoch A and Apweiler R The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res 2000, 28:45-48
13. Boguski MS, Lowe TM and Tolstoshev CM dbEST - database for "expressed sequence tags". Nat Genet 1993, 4:332-333
14. Wang Y, Anderson JB, Chen J, Geer LY, He S, Hurwitz DI, Liebert CA, Madej T, Marchler GH and Marchler-Bauer A MMDB: Entrez's 3D-structure database. Nucleic Acids Res 2002, 30:249-252
15. Wu CH, Huang H, Arminski L, Castro-Alvear J, Chen Y, Hu ZZ, Ledley RS, Lewis KC, Mewes HW and Orcutt BC The Protein Information Resource: an integrated public resource of functional annotation of proteins. Nucleic Acids Res 2002, 30:35-37
16. Marchler-Bauer A, Panchenko AR, Shoemaker BA, Thiessen PA, Geer LY and Bryant SH CDD: a database of conserved domain alignments with links to domain three-dimensional structure. Nucleic Acids Res 2002, 30:281-283
17. The Gene Ontology Consortium Creating the gene ontology resource: design and implementation. Genome Res 2001, 11:1425-1433
18. Ostell JM and Kans JA The NCBI data model. Methods Biochem Anal 1998, 39:121-144
19. Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, Griffiths-Jones S, Howe KL, Marshall M and Sonnhammer EL The Pfam protein families database. Nucleic Acids Res 2002, 30:276-280
20. Letunic I, Goodstadt L, Dickens NJ, Doerks T, Schultz J, Mott R, Ciccarelli F, Copley RR, Ponting CP and Bork P Recent improvements to the SMART domain-based sequence annotation resource. Nucleic Acids Res 2002, 30:242-244
21. Higgins DG and Sharp PM CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene 1988, 73:237-244
22. 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
23. Chung SY and Wong L Kleisli: a new tool for data integration in biology. Trends Biotechnol 1999, 17:351-355