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Bioinformatics Advance Access published online on February 24, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl067
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received December 15, 2005
Revised February 6, 2006
Accepted February 21, 2006

Article

Automated classification of alternative splicing and transcriptional initiation and construction of visual database of classified patterns

Hideki Nagasaki 1 *, Masanori Arita 2, Tatsuya Nishizawa 3, Makiko Suwa 1, and Osamu Gotoh 4

1 Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan
2 Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan; Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8561, Japan
3 Information and Mathematical Science Laboratory, Inc., Tokyo 171-0014, Japan
4 Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan; Department of Intelligence Science and Technology, Graduate School of Informatics, Kyoto University, Kyoto 606-8501, Japan

* To whom correspondence should be addressed.
Hideki Nagasaki, E-mail: h-nagasaki{at}aist.go.jp


  Abstract

Motivation: Large-scale detection and classification of alternative splicing and transcriptional initiation (ASTI) is the first step toward detailed studies of the functional implication and mechanisms of these phenomena.

Results: We have developed an algorithm that classifies all observed units of ASTI into an extendable set of distinct types (e.g., cassette type) by converting a collection of alignments between a genomic DNA sequence and cDNA sequences into binary description. This description system can uniquely and compactly encode not only typical patterns but also any rare patterns that are usually collectively assigned to "others." More than 150 distinct ASTI types were found when this system was applied to genome-wide detection of ASTI units in human and five other eukaryotes.

Availability: The data detected by this system are available through ASTRA {{http://alterna.cbrc.jp/}}, a database equipped with a Java-based browser that can interactively reorganize the order of displayed splicing patterns on demand.

Associate Editor: Alex Bateman
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