Nucleic Acids Research, 2000, Vol. 28, No. 1 228-230
© 2000 Oxford University Press
Increased coverage of protein families with the Blocks Database servers
Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109-1024, USA
The Blocks Database WWW (http://blocks.fhcrc.org ) and Email (blocks@blocks.fhcrc.org ) servers provide tools to search DNA and protein queries against the Blocks+ Database of multiple alignments, which represent conserved protein regions. Blocks+ nearly doubles the number of protein families included in the database by adding families from the Pfam-A, ProDom and Domo databases to those from PROSITE and PRINTS. Other new features include improved Block Searcher statistics, searching with NCBI’s IMPALA program and 3D display of blocks on PDB structures.
* To whom correspondence should be addressed. Tel: +1 206 667 4515; Fax: +1 206 667 5889; Email: steveh@fhcrc.org Present address: Shmuel Pietrokovski, The Weizmann Institute, Rehovot 76100, Israel
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|
|
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|
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|
|
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|
|
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|
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|
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|
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|
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|
|
|
|
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|
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|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
 |
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
R. Apweiler, T. K. Attwood, A. Bairoch, A. Bateman, E. Birney, M. Biswas, P. Bucher, L. Cerutti, F. Corpet, M. D. R. Croning, et al. The InterPro database, an integrated documentation resource for protein families, domains and functional sites Nucleic Acids Res., January 1, 2001; 29(1): 37 - 40. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. H. Haft, B. J. Loftus, D. L. Richardson, F. Yang, J. A. Eisen, I. T. Paulsen, and O. White TIGRFAMs: a protein family resource for the functional identification of proteins Nucleic Acids Res., January 1, 2001; 29(1): 41 - 43. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. A. T. Silverstein, E. Shoop, J. E. Johnson, A. Kilian, J. L. Freeman, T. M. Kunau, I. A. Awad, M. Mayer, and E. F. Retzel The MetaFam Server: a comprehensive protein family resource Nucleic Acids Res., January 1, 2001; 29(1): 49 - 51. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. H. Wu, C. Xiao, Z. Hou, H. Huang, and W. C. Barker iProClass: an integrated, comprehensive and annotated protein classification database Nucleic Acids Res., January 1, 2001; 29(1): 52 - 54. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Murvai, K. Vlahovicek, E. Barta, and S. Pongor The SBASE protein domain library, release 8.0: a collection of annotated protein sequence segments Nucleic Acids Res., January 1, 2001; 29(1): 58 - 60. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Y. Huang and D. L. Brutlag The EMOTIF database Nucleic Acids Res., January 1, 2001; 29(1): 202 - 204. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
 |
|
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|
|
|
|
|
|
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|
|
|
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|
|