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Nucleic Acids Research 2005 33(Web Server Issue):W315-W319; doi:10.1093/nar/gki374
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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

MAVL/StickWRLD for protein: visualizing protein sequence families to detect non-consensus features

William C. Ray*

Children's Research Institute and The Department of Pediatrics, The Ohio State University 700 Children's Drive, Columbus, OH 43205, USA

*Tel: +1 614 355 3522; Fax: +1 614 722 2818; Email: ray{at}biosci.ohio-state.edu

Received February 11, 2005. Revised March 7, 2005. Accepted March 7, 2005.

A fundamental problem with applying Consensus, Weight-Matrix or hidden Markov models as search tools for biosequences is that there is no way to know, from the model, if the modeled sequences display any dependencies between positional identities. In some instances, these dependencies are crucial in correctly accepting or rejecting other sequences as members of the family. MAVL (multiple alignment variation linker) and StickWRLD provide a web-based method to visually survey the model-training sequences to discover and characterize possible dependencies. Initially introduced for nucleic acid sequences, with MAVL/StickWRLD, it is easy to distinguish typical DNA or RNA structural dependencies in input families, identify mixed populations of distinct subfamilies, or discover novel dependencies that result from binding interactions or other selective pressures [W. Ray (2004) Nucleic Acids Res., 32, W59–W63]. Since the announcement of MAVL/StickWRLD for nucleic acids, one of the most requested new features has been the extension of this visualization method to support protein alignments. We are pleased to report that this extension has been successful, that the basic visualization has been augmented in several ways to enhance protein viewing, and that the results with protein alignments are even more dramatic than with NA alignments. MAVL/StickWRLD can be accessed at http://www.microbial-pathogenesis.org/stickwrld/.


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H. G. Ozer and W. C. Ray
MAVL/StickWRLD: analyzing structural constraints using interpositional dependencies in biomolecular sequence alignments.
Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W133 - W136.
[Abstract] [Full Text] [PDF]


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