SpliceSeq 2.1 – Investigate alternative mRNA Splicing in Next Generation mRNA Sequence data

SpliceSeq 2.1

:: DESCRIPTION

SpliceSeq provides a quick, easy method of investigating alternative mRNA splicing in next generation mRNA sequence data. The tool may be used on a single mRNA-Seq sample to identify genes with multiple spliceforms or on a pair of samples to identify differential splicing between the samples. Sequence reads are mapped to splice graphs that unambiguously quantify the inclusion level of each exon and splice junction. The graphs are then traversed to predict the protein isoforms that are likely to result from the observed exon and splice junction reads. UniProt annotations are mapped to each protein isoform to identify potential functional impacts of alternative splicing.

::DEVELOPER

Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center

:: SCREENSHOTS

:: REQUIREMENTS

Linux/Windows/MacOsX
Java

:: DOWNLOAD

SpliceSeq

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Sep 15;28(18):2385-7. Epub 2012 Jul 20.
SpliceSeq: a resource for analysis and visualization of RNA-Seq data on alternative splicing and its functional impacts.
Ryan MC, Cleland J, Kim R, Wong WC, Weinstein JN.

PageMan 0.12 – Annotates, Investigates, and Condenses Microarray data in the Context of Functional Ontologies

PageMan 0.12

:: DESCRIPTION

PageMan is a tool to get a quick overview of multiparallel experiments. PageMan also helps comparing experiments from different organisms.

::DEVELOPER

Max Planck Institute for Molecular Plant Physiology

:: SCREENSHOTS

:: REQUIREMENTS

Windows/Linux/MacOsX
Java

:: DOWNLOAD

PageMan

:: MORE INFORMATION

Citation

Usadel B, Nagel A, Steinhauser D, Gibon Y, Blaesing OE, Redestig H, Sreenivasulu N, Krall L, Hannah MA, Poree F, Fernie AR, Stitt M (2006)
PageMan an interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments,
BMC Bioinformatics 18:7:535

ProDGe 20110509 – Investigate Protein-protein Interactions at the Domain level

ProDGe 20110509

:: DESCRIPTION

ProDGe (Protein Domain Gene) visualizes existing and suggests novel domaindomain interactions and protein-protein interactions at the domain level. The comprehensive dataset behind ProDGe consists of protein, domain and interaction information for both layers, collected and combined appropriately from UniProt, Pfam, DOMINE and IntAct. Based on known domain interactions, ProDGe suggests novel protein interactions and assigns them to four confidence classes, depending on the reliability of the underlying domain interaction. Furthermore, ProDGe is able to identify potential homologous interaction partners in other species, which is particularly helpful when investigating poorly annotated species.

::DEVELOPER

the Center for Bioinformatics Tübingen (Zentrum für Bioinformatik Tübingen, ZBIT).

:: SCREENSHOTS

:: REQUIREMENTS

Linux/ WIndows/MacOsX
Java

:: DOWNLOAD

ProDGe

:: MORE INFORMATION

Citation

Büchel, Finja, Wrzodek, Clemens, Mittag, Florian, Dr?ger, Andreas, Schr?der, Adrian, and Zell, Andreas.
ProDGe: investigating protein-protein interactions at the domain level.
Nature Precedings (2011)