AStalavista pipeline

AStalavista specifications

Information


Unique identifier OMICS_01943
Name AStalavista
Alternative name Alternative Splicing TrAscriptional LAndscape VISualization Tool And more
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Version 4.0
Stability Stable
Source code URL http://sammeth.net/fisheye/browse/Barna/barna.astalavista
Maintained Yes

Subtools


  • ASTA
  • ASTAFUNK
  • SCORER
  • VISTA

Download


Versioning


Add your version

Documentation


Maintainers


  • person_outline Sylvain Foissac <>
  • person_outline Michael Sammeth <>

Additional information


http://sammeth.net/confluence/display/ASTA/1+-+Introduction

Information


Unique identifier OMICS_01943
Name AStalavista
Alternative name Alternative Splicing TrAscriptional LAndscape VISualization Tool And more
Interface Web user interface
Restrictions to use None
Input data A set of transcripts with known exon–intron structure (e.g. from mRNAs or ESTs) or a list of genes/transcripts/proteins IDs.
Input format GTF, TXT
Output data A result page showing a list where each event type is depicted and its unique code in the relative-position notation is given and a graphical overview in form of a pie diagram that displays the distribution of events across the groups, considering differentially each type of simple event and pooling the others in one group.
Output format GTF, ASTA
Computer skills Basic
Stability Stable
Maintained Yes

Subtools


  • ASTA
  • ASTAFUNK
  • SCORER
  • VISTA

Documentation


Maintainers


  • person_outline Sylvain Foissac <>
  • person_outline Michael Sammeth <>

Additional information


http://sammeth.net/confluence/display/ASTA/1+-+Introduction

Publications for Alternative Splicing TrAscriptional LAndscape VISualization Tool And more

AStalavista IN pipeline

2017
PMCID: 5499736
PMID: 28402567
DOI: 10.1093/nar/gkx256

[…] its 5΄-utr region that drives translation of an extra putative protein containing more than 20 residues. in addition, the entire uorf region should be covered by transcriptome sequencing reads., the astalavista algorithm was used to classify as events (46). all as events were further inspected by manually comparing structural differences between splicing isoforms in integrative genomics viewer […]

AStalavista institution(s)
Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; National Laboratory for Scientific Computing, Petrópolis, Rio de Janeiro, Brazil
AStalavista funding source(s)
Supported by the National Counsel of Technological and Scientific Development (CNPq) by grant 132455/2013-7 and 140941/2015-0 as well as grant 310132/2015-0, and from the Research Support Foundation of the State of Rio de Janeiro (FAPERJ) by grant E_06/2015.

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