Bioinformatics Vol. 18 no. 9 2002
Pages 1274-1275
© 2002 Oxford University Press
Applications Note |
A kinase sequence database: sequence alignments and family assignment
1 Department of Cellular and Molecular Pharmacology, University of California, San Francisco, 513 Parnassus, San Francisco, CA 94143-0450, USA
Received on October 9, 2001
; revised on January 2, 2002
; accepted on February 13, 2002
Summary: The Kinase Sequence Database (KSD) located at http://kinase.ucsf.edu/ksd contains information on 290 protein kinase families derived by profile-based clustering of the non-redundant list of sequences obtained from a GenBank-wide search. Included in the database are a total of 5041 protein kinases from over 100 organisms. Clustering into families is based on the extent of homology within the kinase catalytic domain (250–300 residues in length). Alignments of the families are viewed by interactive Excel-based sequence spreadsheets. In addition, KSD features evolutionary trees derived for each family and detailed information on each sequence as well as links to the corresponding GenBank entries. Sequence manipulation tools, such as evolutionary tree generation, novel sequence assignment, and statistical analysis, are also provided.
Availability: The kinase sequence database is a web-based service accessible at http://kinase.ucsf.edu/ksd
Contact: buzko{at}cmp.ucsf.edu shokat{at}cmp.ucsf.edu/ksd
* To whom correspondence should be addressed.
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