ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets.
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.
Foissac
Sylvain
S
Centre de Regulació Genòmica, Barcelona, Spain. sylvain.foissac@crg.es
Sammeth
Michael
M
D017398:Alternative Splicing / Q000235:genetics*; D002874:Chromosome Mapping / Q000379:methods; D019295:Computational Biology / Q000379:methods*; D015342:DNA Probes / Q000235:genetics*; D030541:Databases, Genetic; D016678:Genome; D006801:Humans; D020407:Internet; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation / Q000379:methods*; D022821:RNA Splice Sites / Q000235:genetics*; D012333:RNA, Messenger / Q000378:metabolism; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
D015342:DNA Probes; D022821:RNA Splice Sites; D012333:RNA, Messenger