A kinase sequence database: sequence alignments and family assignment

Oleksandr Buzko; Kevan M Shokat

doi:10.1093/bioinformatics/18.9.1274

A kinase sequence database: sequence alignments and family assignment

Bioinformatics. 2002 Sep;18(9):1274-5. doi: 10.1093/bioinformatics/18.9.1274.

Authors

Oleksandr Buzko¹, Kevan M Shokat

Affiliation

¹ Department of Cellular and Molecular Pharmacology, University of California, San Francisco, 513 Parnassus, San Francisco, CA 94143-0450, USA. buzko@cmp.ucsf.edu

PMID: 12217924
DOI: 10.1093/bioinformatics/18.9.1274

Abstract

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 5,041 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@cmp.ucsf.edu; shokat@cmp.ucsf.edu/ksd

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Cluster Analysis
Database Management Systems*
Databases, Protein*
Information Storage and Retrieval / methods
Internet
Protein Kinases / classification*
Protein Kinases / genetics*
Sequence Alignment / methods*
Sequence Analysis, Protein / methods*
Sequence Homology

Substances

Protein Kinases