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Nucleic Acids Research Advance Access originally published online on May 7, 2007
Nucleic Acids Research 2007 35(Web Server issue):W297-W299; doi:10.1093/nar/gkm311
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Nucleic Acids Research, 2007, Vol. 35, No. suppl_2 W297-W299
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets

Sylvain Foissac* and Michael Sammeth

Centre de Regulació Genòmica, Barcelona, Spain

*To whom correspondence should be addressed. Tel: +34 933 160 166; Fax: +34 933 969 983; Email: sylvain.foissac{at}crg.es

Received January 31, 2007. Revised April 6, 2007. Accepted April 14, 2007.

In the process of establishing more and more complete annotations of eukaryotic genomes, a constantly growing number of alternative splicing (AS) events has been reported over the last decade. Consequently, the increasing transcript coverage also revealed the real complexity of some variations in the exon–intron structure between transcript variants and the need for computational tools to address ‘complex’ AS events. ASTALAVISTA (alternative splicing transcriptional landscape visualization tool) employs an intuitive and complete notation system to univocally identify such events. The method extracts AS events dynamically from custom gene annotations, classifies them into groups of common types and visualizes a comprehensive picture of the resulting AS landscape. Thus, ASTALAVISTA can characterize AS for whole transcriptome data from reference annotations (GENCODE, REFSEQ, ENSEMBL) as well as for genes selected by the user according to common functional/structural attributes of interest: http://genome.imim.es/astalavista


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F. Birzele, R. Kuffner, F. Meier, F. Oefinger, C. Potthast, and R. Zimmer
ProSAS: a database for analyzing alternative splicing in the context of protein structures
Nucleic Acids Res., January 1, 2008; 36(suppl_1): D63 - D68.
[Abstract] [Full Text] [PDF]


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