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Nucleic Acids Research 2005 33(Web Server Issue):W267-W270; doi:10.1093/nar/gki465
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© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

MINER: software for phylogenetic motif identification

David La and Dennis R. Livesay1,2,*

Department of Biological Sciences, California State Polytechnic University Pomona, CA 91767, USA 1Department of Chemistry, California State Polytechnic University Pomona, CA 91767, USA 2Center for Macromolecular Modeling and Materials Design, California State Polytechnic University Pomona, CA 91767, USA

*To whom correspondence should be addressed. Tel: +1 909 869 4409; Fax: +1 909 869 4344; Email: drlivesay{at}csupomona.edu

Received February 11, 2005. Revised March 25, 2005. Accepted April 13, 2005.

MINER is web-based software for phylogenetic motif (PM) identification. PMs are sequence regions (fragments) that conserve the overall familial phylogeny. PMs have been shown to correspond to a wide variety of catalytic regions, substrate-binding sites and protein interfaces, making them ideal functional site predictions. The MINER output provides an intuitive interface for interactive PM sequence analysis and structural visualization. The web implementation of MINER is freely available at http://www.pmap.csupomona.edu/MINER/. Source code is available to the academic community on request.


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K. C. Dukka Bahadur and D. R. Livesay
Improving position-specific predictions of protein functional sites using phylogenetic motifs
Bioinformatics, October 15, 2008; 24(20): 2308 - 2316.
[Abstract] [Full Text] [PDF]


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