Contact: Tyler Alioto (tyler.alioto@crg.es)

Back to the course homepage: /courses/Pamplona07/

The AStalavista web server extracts and displays alternative splicing (AS) events from a given genomic annotation of exon-intron gene coordinates.

By comparing all given transcripts, AStalavista detects the variations in their splicing structure and identify all AS events (like exon skipping, alternate donor, etc) by assigning to each of them an AS code. AStalavista provides a visual summary of the AS landscape in the analyzed dataset, the possibility to browse the results on the UCSC website or to download them in GTF or ASTA format. You can use AStalavista for any genome by providing your own annotation set, the identifier of your gene(s) of interest, or analyze the AS landscape of reference annotation datasets like Gencode, RefSeq, Ensembl, FlyBase,... Example:

1. Go to: /astalavista/
2. Click on "EXAMPLE2", two gene names appear in the box (RNPC2 and CDC2)
3. "SUBMIT QUERY"
4. Wait for astalavista to extract the corresponding transcripts, to perform all pairwise comparisons and find all alternative splicing events.
5. Check the results, the distribution of alternative splicing events is presented in a pie diagram, each type of event is described underneath.
6. Click on a "show event details" to see all occurrence of the pictured event, a link to the UCSC genome browser allows to check the genomic region that is involved.
7. To see the same for all genes from the refseq annotation, come back to the main page (1.), clear the previous query and select "refseq" in the "use a known annotation" field. Run AStalavista as before.