Bioinformatics, Vol 15, 376-381, Copyright © 1999 by Oxford University Press
A Chou and J Burke
MOTIVATION: DNA sequence clustering has become a valuable method in support
of gene discovery and gene expression analysis. Our interest lies in
leveraging the sequence diversity within clusters of expressed sequence
tags (ESTs) to model gene structure for the study of gene variants that
arise from, among other things, alternative mRNA splicing, polymorphism,
and divergence after gene duplication, fusion, and translocation events. In
previous work, CRAW was developed to discover gene variants from assembled
clusters of ESTs. Most importantly, novel gene features (the differing
units between gene variants, for example alternative exons, polymorphisms,
transposable elements, etc.) that are specialized to tissue, disease,
population, or developmental states can be identified when these tools
collate DNA source information with gene variant discrimination. While the
goal is complete automation of novel feature and gene variant detection,
current methods are far from perfect and hence the development of effective
tools for visualization and exploratory data analysis are of paramount
importance in the process of sifting through candidate genes and validating
targets. RESULTS: We present CRAWview, a Java based visualization extension
to CRAW. Features that vary between gene forms are displayed using an
automatically generated color coded index. The reporting format of CRAWview
gives a brief, high level summary report to display overlap and divergence
within clusters of sequences as well as the ability to 'drill down' and see
detailed information concerning regions of interest. Additionally, the
alignment viewing and editing capabilities of CRAWview make it possible to
interactively correct frame-shifts and otherwise edit cluster assemblies.
We have implemented CRAWview as a Java application across windows NT/95 and
UNIX platforms. AVAILABILITY: A beta version of CRAWview will be freely
available to academic users from Pangea Systems
(http://www.pangeasystems.com). Contact :
ARTICLES
CRAWview: for viewing splicing variation, gene families, and polymorphism in clusters of ESTs and full-length sequences
Genome Informatics Group, Pangea Systems, 1999 Harrison Street, Suite 1100, Oakland, CA 94612, USA.
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