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Nucleic Acids Research Advance Access originally published online on May 27, 2009
Nucleic Acids Research 2009 37(Web Server issue):W452-W458; doi:10.1093/nar/gkp409
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Nucleic Acids Research, 2009, Vol. 37, No. suppl_2 W452-W458
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

PLecDom: a program for identification and analysis of plant lectin domains

Smriti Shridhar, Debasis Chattopadhyay and Gitanjali Yadav*

Computational Biology Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India

*To whom correspondence should be addressed. Tel: +91 11 26735103; Fax: +91 11 26741658; Email: gy{at}nipgr.res.in

Received February 16, 2009. Revised April 25, 2009. Accepted May 2, 2009.

PLecDom is a program for detection of Plant Lectin Domains in a polypeptide or EST sequence, followed by a classification of the identified domains into known families. The web server is a collection of plant lectin domain families represented by alignments and profile Hidden Markov Models. PLecDom was developed after a rigorous analysis of evolutionary relationships between available sequences of lectin domains with known specificities. Users can test their sequences for potential lectin domains, catalog the identified domains into broad substrate classes, estimate the extent of divergence of new domains with existing homologs, extract domain boundaries and examine flanking sequences for further analysis. The high prediction accuracy of PLecDom combined with the ease with which it handles large scale input, enabled us to apply the program to protein and EST data from 48 plant genome-sequencing projects in various stages of completion. Our results represent a significant enrichment of the currently annotated plant lectins, and highlight potential targets for biochemical characterization. The search algorithm requires input in fasta format and is designed to process simultaneous connection requests from multiple users, such that huge sets of input sequences can be scanned in a matter of seconds. PLecDom is available at http://www.nipgr.res.in/plecdom.html.


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