tappAS 0.99.15 – Understand the Functional Implications of Alternative Splicing

tappAS 0.99.15

:: DESCRIPTION

tappAS is a Java GUI application for the analysis of RNA-Seq data down to the isoform level.It provides a comprehensive set of data analysis, visualization, filtering, and hoc query tools.It will run on most modern computers, provided they have enough computational resources and storage.

::DEVELOPER

The Genomics of Gene Expression Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java
  • R package

:: DOWNLOAD

 tappAS

:: MORE INFORMATION

 

SpliceInfo – Information Repository for mRNA Alternative Splicing in Human Genome

SpliceInfo

:: DESCRIPTION

SpliceInfo is an information repository to collect the occurrences of the four major alternative-splicing (AS) modes in human genome; these include exon skipping, 5′-alternative splicing, 3′-alternative splicing and intron retention.

::DEVELOPER

SpliceInfo team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D80-5.
SpliceInfo: an information repository for mRNA alternative splicing in human genome.
Huang HD, Horng JT, Lin FM, Chang YC, Huang CC.

AStalavista 3.2 – Alternative Splicing Transcriptional Landscape Visualization tool

AStalavista 3.2

:: DESCRIPTION

AStalavista (the Alternative Splicing Trascriptional Landscape Visualization Tool) retrieves all alternative splicing events from generic transcript annotations.

::DEVELOPER

Genome BioInformatics Research Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX/Windows
  • Java 

:: DOWNLOAD

 AStalavista

:: MORE INFORMATION

Citation

Sammeth M, Foissac S, Guigó R (2008)
A General Definition and Nomenclature for Alternative Splicing Events.
PLoS Comput Biol 4(8): e1000147.

SplicingViewer 1.1.0 – Detection, Annotation and Visualization of the Alternative Splicing from RNA-Seq Data

SplicingViewer 1.1.0

:: DESCRIPTION

SplicingViewer is an integrated tool which can detect the splice junctions based on known gene models, annotate the alternative splicing patterns based on the splice junctions, and visualize the patterns of alternative splicing events. In addition, as a viewer, SplicingViewer can also be used to display the RNA-Seq reads mapping results with high speed and lower memory spend.

::DEVELOPER

SplicingViewer team

:: SCREENSHOTS

SplicingViewer

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 SplicingViewer

:: MORE INFORMATION

Citation

Genomics. 2012 Mar;99(3):178-82. doi: 10.1016/j.ygeno.2011.12.003. Epub 2011 Dec 28.
Detection, annotation and visualization of alternative splicing from RNA-Seq data with SplicingViewer.
Liu Q, Chen C, Shen E, Zhao F, Sun Z, Wu J.

ASpipe 2.1.8 – Process GeneSeqer/GMAP Alignments & Identify Alternative Splicing

ASpipe 2.1.8

:: DESCRIPTION

ASpipe (alternative splicing) is a pipeline to process GeneSeqer/GMAP alignments and identify alternative splicing (AS) events from the alignments.ASpipe extracts coordinates and scores for high-quality intron/exon/alignments from the original program outputs and stores them in MySQL5.0 databases.

::DEVELOPER

The Brendel Group @ Indiana University

:: REQUIREMENTS

:: DOWNLOAD

ASpipe

:: MORE INFORMATION

Citation

Wang, B.-B., O’Toole, M., Brendel, V. & Young, N.D. (2008)
Cross-species EST alignments reveal novel and conserved alternative splicing events in legumes.
BMC Plant Biol. 8:17.