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Nucleic Acids Res. 2007 Jul;35(Web Server issue):W297-9. Epub 2007 May 7.

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

Author information

1
Centre de Regulació Genòmica, Barcelona, Spain. sylvain.foissac@crg.es

Abstract

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.

PMID:
17485470
PMCID:
PMC1933205
DOI:
10.1093/nar/gkm311
[Indexed for MEDLINE]
Free PMC Article

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