MAVL and StickWRLD: visually exploring relationships in nucleic acid sequence alignments
Children's Research Institute and the Department of Pediatrics, The Ohio State University, 700 Children's Drive, W531, Columbus, OH 43205, USA
* Tel: +1 614 722 2557; Fax: +1 614 722 3273; Email: ray{at}biosci.ohio-state.edu
Received February 16, 2004; Revised April 19, 2004; Accepted April 29, 2004
Many powerful tools have been created to detect and describe the similarities between nucleic acid or protein sequences. Frequently these take the form of a sequence consensus, expressing simple most popular positional identities, positional identities with allowances for varying positions or some type of statistical description of the positional frequency characteristics of the defining sequence family. Despite the fact that some provide intuitively interpretable descriptions of the consensuses themselves, they typically do not give the viewer any information about regions of the sequence that might have inter-positional dependencies, and that therefore do not obey a strict consensus behavior. Herein, we present MAVL (Multiple Alignment Variation Linker) and StickWRLD. MAVL is our web-based application for detecting and displaying both positive and negative inter-positional correlations in nucleic acid sequences. MAVL examines all positional pairs in each of a collection of pre-aligned sequences and determines any pairs that occur with either greater or lesser frequency than a positional frequency matrix would predict. These data are then composited into a StickWRLD representation and supplied back to the user as a VRML (virtual reality modeling language) file. MAVL and StickWRLD can be accessed at http://www.microbial-pathogenesis.org/stickwrld/. A tutorial that explains MAVL features and demonstrates typical user interactions with StickWRLD graphs is available at http://www.microbial-pathogenesis.org/stickwrld/tutorial/sticktut2.html. This tutorial is quite large; please be patient while it loads.
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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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W. C. Ray MAVL/StickWRLD for protein: visualizing protein sequence families to detect non-consensus features Nucleic Acids Res., July 1, 2005; 33(suppl_2): W315 - W319. [Abstract] [Full Text] [PDF]
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