Genome BioInformatics Research Lab

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- AStalavista web server -
Alternative Splicing transcriptional landscape visualization tool
 
 

Attention
From version 3.0 on, the new AStalavista codebase is maintained at sammeth.net/confluence/display/ASTA. Please go there to download the most recent version of the library, for the time being the page here maintains the old AStalavista server version, i.e., for pairwise events.

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 vizual 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,...

For more information, please have a look at our FAQ or check out the RSS News Feed RSS 2.0 .


Input

Choose your organism (and genome assembly version):  

To provide the annotation, you can use a genome-wide reference annotation and/or specify your own set of genes:

- Use a known annotation:     [?]
    OR/AND
- Provide your own dataset, either a gtf annotation [?] or a list of genes/transcripts/proteins (one ID per line)[?]:
   Upload it from your computer  
     or
   Paste it in this box   [?] [?]

[?] [?]


Options

Consider:
all provided transcripts (default)   coding transcripts only (with CDS)   non-coding transcripts only (without CDS)
all AS events (default)   coding AS events only (strictly included in CDS)   non-coding AS events (not affecting the CDS)

Output format:
GTF format   ASTA format  

[?] [?]

Download

To download the latest version, click here: Download
From version 3.0 on, the new AStalavista codebase is available at sammeth.net/confluence/display/ASTA, go there to download the most recent version of the library.

Version history

09/03/09 2.2

Bugfixes in I/O for different platforms (e.g., sorting routine -- see bugtracker).

23/08/08 2.1

Basic command line interface for the graph based retrieval of AS events is available (i.e., --command asta).

Please file rigurously all bugs and recommendations in the bugtracking system at sammeth.net/jira.
Before you file a new ticket, please check the current list of issues.

FAQ / Video

The AStalavista Frequently Asked Questions are here.

To get an idea of the main concept, you may first want to watch the AStalavista video at
SciVee
http://www.scivee.tv/node/6837

Publications

Foissac S, Sammeth M (2007) ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets. Nucleic Acids Research 35 (Web Server issue): W297-299

Sammeth M, Foissac S, Guigó R (2008) A general definition and nomenclature for alternative splicing events. PLoS Computational Biology 4(8): e1000147 doi:10.1371/journal.pcbi.1000147

Sammeth M (2009) Complete alternative splicing events are bubbles in splicing graphs. Journal of Computational Biology 16: 1117-1140

Corrigendum—a reprint containing all corrections listed below is available at the link above. Thanks to the thouroughful readers pointing these out!
»legend of Figure 1: the dimension of the depicted event is d=12 with the pattern composed by variants as shown
1[4^8–12], 1[4^10–12], 1[4^11–12], 1[4^13–15^16–17^18–19], 1[4^13–15^18–19], 1[4^14–15^16–17^18–19],
1[4^14–15^18–19], 2[12], 3[4^11–12], 5(7^8–9), 6[7^11–12], 6[7^13–15^18–19]
»Figure 3: missing complete event with alternative acceptor
»Figure 8: boundaries of the box in the boxplot coincide obviously the boundaries of the 1st respectively the 3rd quartile,
whereas the box contains the two quartiles around the median. Text is adjusted for sensitive readers.
»Acknowledgements: some formating errors with Names.

Supplementary Data Files with events used for the analysis in this publication
human (hg18)human (hg18)
DimensionRefSeq          RefSeq+mRNA   RefSeq+mRNA+ESTs   RefSeq          RefSeq+mRNA   RefSeq+mRNA+ESTs   
d=2 9,477 events 34,603 events 134,875 events 2,638 events 19,127 events 52,508 events
d=3 7,173 events 17,294 events 97,193 events 2,669 events 4,839 events 15,896 events
d=4 21,620 events 43,476 events 153,292 events 9,321 events 10,570 events 17,025 events
complete 6,493 events 26,412 events 91,117 events 1,787 events 16,184 events 42,198 events



Authors and acknowledgements

The method, software and server have been designed and implemented by Michael Sammeth, Sylvain Foissac and Roderic Guigo.
Thanks to the GBL people for their help.
Any question and/or comment? Please let us know:
sylvain.foissac a t crg.es
micha a t sammeth.net

 
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