Bioinformatics Advance Access published online on February 24, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl067
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
1 Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan
* To whom correspondence should be addressed.
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.
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
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
Hideki Nagasaki, E-mail: h-nagasaki{at}aist.go.jp
Abstract
Associate Editor: Alex Bateman
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  O. Gotoh A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence Nucleic Acids Res., May 1, 2008; 36(8): 2630 - 2638. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Bhasi, R. V. Pandey, S. P. Utharasamy, and P. Senapathy EuSplice: a unified resource for the analysis of splice signals and alternative splicing in eukaryotic genes Bioinformatics, July 15, 2007; 23(14): 1815 - 1823. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Foissac and M. Sammeth ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets Nucleic Acids Res., July 13, 2007; 35(suppl_2): W297 - W299. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Hiller, S. Nikolajewa, K. Huse, K. Szafranski, P. Rosenstiel, S. Schuster, R. Backofen, and M. Platzer TassDB: a database of alternative tandem splice sites Nucleic Acids Res., January 12, 2007; 35(suppl_1): D188 - D192. [Abstract] [Full Text] [PDF]
|
|