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

Linux
MySQL
Perl

:: 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.

AStalavista 4.0.1 – Alternative Splicing Transcriptional Landscape Visualization tool

AStalavista 4.0.1

:: DESCRIPTION

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

::DEVELOPER

RODERIC GUIGO LAB

:: 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

:: 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.

PSGInfer 1.2.1 – Inference of Alternative Splicing from RNA-Seq data with probabilistic Splice Graphs

PSGInfer 1.2.1

:: DESCRIPTION

PSGInfer (Probabilistic Splice Graph Inference) analyzes RNA-Seq data with probabilistic splice graph models of alternative RNA processing (transcription initiation, splicing, and polyadenylation).

::DEVELOPER

Laura H. LeGault , Colin Dewey

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

PSGInfer

:: MORE INFORMATION

Citation

Laura H. LeGault and Colin N. Dewey. (2013)
Inference of alternative splicing from RNA-Seq data with probabilistic splice graphs.
Bioinformatics. 29(18):2300-2310.

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

Citation

tappAS: a comprehensive computational framework for the analysis of the functional impact of differential splicing
Lorena de la Fuente, et al.
bioRxiv 690743; doi: https://doi.org/10.1101/690743