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Nucleic Acids Research 2006 34(Web Server issue):W133-W136; doi:10.1093/nar/gkl251
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© The Author 2006. 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@oxfordjournals.org

Article

MAVL/StickWRLD: analyzing structural constraints using interpositional dependencies in biomolecular sequence alignments

Hatice Gulcin Ozer and William C. Ray1,*

Biophysics Graduate Program, The Ohio State University 700 Children's Drive. Columbus, OH 43205, USA 1 Children's Research Institute and The Department of Pediatrics, The Ohio State University 700 Children's Drive. Columbus, OH 43205, USA

*To whom correspondence should be addressed. Tel: +1 614 355 3522; Fax: +1 614 722 2818; Email: ray.29{at}osu.edu

Received February 14, 2006. Revised March 1, 2006. Accepted March 30, 2006.

The increasing availability of structurally aligned protein families has made it possible to use statistical methods to discover regions of interpositional dependencies of residue identity. Such dependencies amongst residues often have structural or functional implications, and their discovery can supply valuable constraints that assist in the refinement of measured, or predicted molecular structure assignments. Multiple Alignment Variation Linker (MAVL) and StickWRLD [W. Ray (2004) Nucleic Acids Res., 32, W59–W63] were developed to analyze and visualize nucleic acid and protein alignments, to discover and illuminate position/location relationships to the user. The original system analyzed users' data from a web-form submission and presented the user with a static VRML diagram describing their data. We are pleased to report that MAVL/StickWRLD has been completely redesigned and rewritten. MAVL/StickWRLD now functions as a platform-independent Java applet, with real-time dynamic controls that enable much more intuitive exploration and interaction with the data. The system has also been upgraded to enable visualization of a range of aggregate residue properties, and an extensive database of pre-computed StickWRLD diagrams based on PFAM families is now available directly from the interface. The Java StickWRLD applet is available via the WWW at http://www.microbial-pathogenesis.org/stickwrld/.


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