PRODOC: a resource for the comparison of tethered protein domain architectures with in-built information on remotely related domain families

Krishnadev, O and Rekha, N and Pandit, SB and Abhiman, Saraswathi and Mohanty, S and Swapna, LS and Gore, S and Srinivasan, N (2005) PRODOC: a resource for the comparison of tethered protein domain architectures with in-built information on remotely related domain families. In: Nucleic Acids Research, 33 (Web Se). W126-W129.

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Abstract

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 approximately $\sim$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.

Item Type:	Journal Article
Publication:	Nucleic Acids Research
Publisher:	Oxford University Press
Additional Information:	The Copyright belongs to Oxford University Press.
Department/Centre:	Division of Biological Sciences > Molecular Biophysics Unit Division of Interdisciplinary Sciences > Supercomputer Education & Research Centre
Date Deposited:	03 Mar 2006
Last Modified:	22 Feb 2019 05:46
URI:	http://eprints.iisc.ac.in/id/eprint/5637

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