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PRODOC: a resource for the comparison of tethered protein domain architectures with in-built information on remotely related domain families
Molecular Biophysics Unit, Indian Institute of Science Bangalore 560 012, India 1Super Computer Education and Research Center, Indian Institute of Science Bangalore 560 012, India
*To whom correspondence should be addressed. Tel: +91 80 2293 2837; Fax: +91 80 2360 0535; Email: ns{at}mbu.iisc.ernet.in
Received February 13, 2005. Revised March 23, 2005. Accepted April 15, 2005.
PROtein Domain Organization and Comparison (PRODOC) comprises several programs that enable convenient comparison of proteins as a sequence of domains. The in-built dataset currently consists of 
698 000 proteins from 192 organisms with complete genomic data, and all the SWISSPROT proteins obtained from the Pfam database. All the entries in PRODOC are represented as a sequence of functional domains, assigned using hidden Markov models, instead of as a sequence of amino acids. On average 69% of the proteins in the proteomes and 49% of the residues are covered by functional domain assignments. Software tools allow the user to query the dataset with a sequence of domains and identify proteins with the same or a jumbled or circularly permuted arrangement of domains. As it is proposed that proteins with jumbled or the same domain sequences have similar functions, this search tool is useful in assigning the overall function of a multi-domain protein. Unique features of PRODOC include the generation of alignments between multi-domain proteins on the basis of the sequence of domains and in-built information on distantly related domain families forming superfamilies. It is also possible using PRODOC to identify domain sharing and gene fusion events across organisms. An exhaustive genome–genome comparison tool in PRODOC also enables the detection of successive domain sharing and domain fusion events across two organisms. The tool permits the identification of gene clusters involved in similar biological processes in two closely related organisms. The URL for PRODOC is http://hodgkin.mbu.iisc.ernet.in/~prodoc.
Present addresses: S. B. Pandit, Center of Excellence in Bioinformatics, University at Buffalo, New York, USA
S. Abhiman, Centre for Genomics and Bioinformatics, Karolinska Institutet, Stockholm, Sweden
S. Gore, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, UK
The authors wish it to be known that, in their opinion, the first three authors should be regarded as joint First Authors
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