Genome BioInformatics Research Lab
Help  |  News  |  People  |  Research    Software    Publications  |  Links
Resources & Datasets  |  Gene Predictions  |  Seminars & Courses

  IMIM * UPF * CRG * GRIB HOME Software AStalavista
 
- AStalavista web server -
Alternative Splicing transcriptional landscape visualization tool
  
 

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

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.
Before you file a new bug, please check the current list of bugs (Reports: All bugs in the menu to your left hand) or alternatively search hem with the "Summary (contains)" field given in the mask at Search: Detailed Search (scroll all the way down). If you don't find your scenario already described there, use Welcome: Submit bug to add a new report. Specify the application \quot;AStalavista\quot; and the version you use, afterwards give a brief description of your observation. In the "Description" field, specify your platform (e.g., Windows XP, SuSe Linux, Mac OSX PowerPC, etc. ...) and a more detailed description of the problem, for instance, about the input files and parameters you used, the reproducibility of the error and so on. You may leave your name and/or email to help me synchronizing eventual email correspondence. Try to assign a severity level according to how crucial you estimate the error, e.g., wrong output=HIGH, additional feature recommendation= LOW, something in between=MEDIUM, ... , a SHOWSTOPPER would be assigned in cases of a program crash or deadlock. Please also provide the version number of the respective FLUX module you use - refer to the program manuals - in case you are not sure, you may also provide the approximate date you aquired/downloaded it.

Email Address

Password

 

Depending on your configuration you may have to hit "Login" - if there is an error go back in your browser and turn to press the "Login" on this page. Alternatively, you may wish to go to the BugHost Login page http://www.bughost.com/login.asp and login using the corresponding email (bugs a t sammeth.net) and password (nobugs).

Clicking the login button signifies my acceptance of the terms listed in the license agreement.

NOTE: in case your browser gives you another login form after pressing "Login", either go back to this page and press "Login" a second time or use following data in the new mask.

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

 
  Disclaimer webmaster