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Bioinformatics Vol. 17 no. 8 2001
Pages 748-749
© 2001 Oxford University Press

Applications Note

HOMSTRAD: adding sequence information to structure-based alignments of homologous protein families

P. I. W. de Bakker 1, A. Bateman 2, D. F. Burke 1, R. N. Miguel 1, K. Mizuguchi 1, J. Shi 1, H. Shirai 1 and T. L. Blundell 1

1 Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
2 The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK

Received on February 20, 2001 ; revised on March 30, 2001 ; accepted on April 6, 2001

Summary: We describe an extension to the Homologous Structure Alignment Database (HOMSTRAD; Mizuguchi et al. , Protein Sci. , 7, 2469–2471, 1998a) to include homologous sequences derived from the protein families database Pfam (Bateman et al. , Nucleic Acids Res. , 28, 263–266, 2000). HOMSTRAD is integrated with the server FUGUE (Shi et al. , submitted, 2001) for recognition and alignment of homologues, benefitting from the combination of abundant sequence information and accurate structure-based alignments.

Availability: The HOMSTRAD database is available at: http://www-cryst.bioc.cam.ac.uk/homstrad/. Query sequences can be submitted to the homology recognition/alignment server FUGUE at: http://www-cryst.bioc.cam.ac.uk/fugue/.

Contact: homstrad{at}cryst.bioc.cam.ac.uk


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