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Alternative Splicing transcriptional landscape visualization tool
The AStaLaVISta FAQs
AS is used for Alternative Splicing.
It stands for alternative splicing and transcriptional landscape visualization tool.
The CDS refer to the Coding DNA Sequence, defined by the part of a given mature transcript that is translated into protein, from the start codon to the stop codon.
This refers to the version of the human genome assembly and determines the version of the corresponding reference annotations (check the NCBI or UCSC website for more details). If you provide some custom annotation, you should check for compatibility with your genomic coordinates. Note that as AStaLAviSta is an independant system, the AS landscape would not be affected as long as you do not mix different versions of genome assembly in the same input. The external links to the UCSC browser may be, though.
First, there is no formal definition for the traditional nomenclature, usually just illustrated with simple schemes. This can induce some incertitude. For instance, we commonly use the term exon skipping. But not only. What about cassette exon, retained exon, or just alternative exon? Do these terms refer to the same biological event? Otherwise, are the differences clear for everybody? There is obviously a problem of semantic in AS.
To each AS event is assigned an AS code according to the relative position of the alternative splice sites that are involved in the splicing variation.
An exon skipping event has the AS code
The AS code for two competetive donor sites is
Alternative acceptor sites are denoted by
The AS code of intron retention events is
A file format description is available here
As described above, AStalavista extracts AS events dynamically from any given annotation, regardless of the species the annotation is from. However, since the GTF file format intrinsicly does not provide information about the species (respectively, the genome build), AStalavista needs this information in order to synchronize with the UCSC genome browser for proper visualization of the extracted events.
No. The selection possibilities in the "organism" field represent the most recent genome builds from popular species that can be browsed at the UCSC genome browser. If your transcript annotation is from a species/genome build that is not in the list, please select "-other-". Consequently, you will not be able to use the UCSC genome browser for visualization, but AS events will be extracted in normal fashion. If you would like to have an organism added to the list, please contact the authors.
AStalavista currently provides popular annotations (e.g., RefSeq) for some of the popular genomes (currently: human, mouse, fruitfly and worm). If you would like to analyze the AS landscape of a known annotation dataset, you can provide a gtf file to astalavista (to get this file, see next question) or ask the authors at sylvain.foissac<at>crg. es
You can go to the UCSC table browser, where you have to select the desired clade/species/genome assembly, and to specify GTF as "output format". Another possibility is the EnsEmbl Biomart datamining tool, where after selecting the "Dataset" (i.e., the organism) and the "Database" (fixing the genome build), you have to select "Attributes" - "Structures", and finally under "Results" to specify "GFF" in the "rows as" selection box.
To extract AS events, AStalavista needs an input. If you can/do not select a predefined one, an annotation file or list of gene/protein identifiers is to be provided for the selected organism.
AStalavista allows for this in order to investigate for the enrichment of existing annotations. If you select a predefined annotation and you paste a custom annotation in the corresponding box, both annotation files will be concatenated and investigated together. In this case, please ensure that the annotation you provide is from the same species/genome build as the annotation predefined on AStalavista.
This option is available for the species/genome builds with predefined annotations. In order to run AS analysis exclusively on a set of genes/transcripts, you select one of those species (i.e., human, mouse, fruitfly or worm), you leave the "annotation" selection empty and paste the corresponding list of identifiers in the input box. AStalavista is currently providing various naming systems (incl. RefSeq, EnsEmbl, Gene symbols, SwissProt, etc.), however, if you wish to suggest of including additional nomenclatures, contact the authors at sylvain.foissac<at>crg. es.
This will result in a request for a complete genome analysis using the corresponding predefined annotation, taking additionally into account the genes/transcripts as identified by the identifiers. Consequently, generating the results may take comparatively long (i.e., several minutes), also dependent on the current server load. However, it enables to mix transcripts/genes from another annotation into one of the provided reference annotations.
In order to avoid long waiting times on a fixed input like the provided annotation files, AStalavista provides precomputed results here. Clearly, this is no longer possible when provided reference annotations are mixed with custom input, e.g., additional annotations or gene/transcript/protein identifier lists.
Yes, but if the transcript is new (no ID), you need to know the genomic coordinates of the exon-intron structure.
Here are the exhaustive list of the identifiers we handle for each species (gene/transcript/protein):
We try our best to keep the webserver up to date, but the downloadable program versions are always more recent than the webserver. In case you encounter differences, the events shown by the webserver should always be a subset of the ones found by the executable in the download bundle. However, if you have the impression that something is fishy with your output, file a bug report or contact us.