MetaFam: A unified classification of protein families. I. Overview and statistics

Bioinformatics

Volumn 17, Issue 3, 2001, Pages 249-261

  Silverstein, K A T ^a   Shoop, E ^a   Johnson, J E ^a   Retzel, E F ^a  

^a University of Minnesota   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; AUTOMATION; CLASSIFICATION; COMPUTER PROGRAM; CONTROLLED STUDY; DATA BASE; FAMILY SIZE; GENE SEQUENCE; MATHEMATICAL COMPUTING; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN FAMILY; STATISTICS; THEORY;

EID: 0035075436     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/17.3.249     Document Type: Article

References (38)

1. Gapped blast and psi-blast: A new generation of protein database search programs
2. InterPro-an integrated documentation resource for protein families, domains, and functional sites
3. PRINTS-S: The database formerly known as PRINTS
4. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000
5. The Protein Information Resource (PIR)
6. The Pfam protein families database
7. GenBank
8. Combining many multiple alignments in one improved alignment
9. ProDom and ProDom-CG: Tools for protein domain analysis and whole genome comparisons
10. A model of evolutionary change in proteins
11. A comparison of sequence and structure protein domain families as a basis for structural genomics
12. Automated protein sequence database classification. I. Integration of compositional similarity search, local similarity search, and multiple sequence alignment
13. Automated protein sequence database classification. II. Delineation of domain boundaries from sequence similarities
14. Profile analysis: Detection of distantly related proteins
15. Increased coverage of protein families with the blocks database servers
16. Amino acid substitution matrices from protein blocks
17. Embedding strategies for effective use of information from multiple sequence alignments
18. Blocks+: A non-redundant database of protein alignment blocks derived from multiple compilations
19. Protein classification and functional assignment
20. The PROSITE database, its status in 1999
21. Protein folds and families: Sequence and structure alignments
22. ProClass protein family database
23. SCOP: A structural classification of proteins database
24. The SYSTERS protein sequence cluster set
25. Hidden Markov Models in computational biology: Applications to protein modeling
26. HOMSTRAD: A database of protein structure alignments for homologous families
27. The SBASE protein domain library, release 7.0: A collection of annotated protein sequence segments
28. The CATH database provides insights into protein structure/function relationships
29. ADSP-a new package for computational sequence analysis
30. SMART: A web-based tool for the study of genetically mobile domains
31. MetaFam: A unified classification of protein families. II. Schema and query capabilities
32. A database of globular protein structural domains: Clustering of representative family members into similar folds
33. Database of protein sequence alignments: PIR-ALN
34. PIR-ALN: A database of protein sequence alignments
35. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
36. A comprehensive comparison of multiple sequence alignment programs
37. A re-estimation for the total numbers of protein folds and superfamilies
38. ProtoMap: Automatic classification of protein sequences and hierarchy of protein families