This is the Linux app named ISVASE to run in Linux online whose latest release can be downloaded as ISVASE1.1.tar.gz. It can be run online in the free hosting provider OnWorks for workstations.
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ISVASE to run in Linux online
DESCRIPTION
To generate correct mature mRNAs, the exons must be identified and joined together precisely and efficiently by RNA splicing mechanism. It is to be noted that about one third or a half of all disease-causing mutations effect RNA splicing. However, there is little bioinformatics tools to directly identify sequence variants associated with splicing events (SVASE) based on RNA-seq data. We developed ISVASE, a simple and convenient tool for identifying SVASE directly using RNA-seq data. Comparing with the existing software PVAAS, our method has several advantages such as stringent rule-depended filters and statistical filters in each step, detection sequence variants for known splicing events, identification sequence variants in two parts of splicing (junction) separately, detection junction shift events if providing known splicing annotation, evaluating splicing signal, comparing with known DNA mutation and/or RNA editing data, and short running time.Features
- It is the first tool to identify sequence variant associated with splicing event for both new splicing variants and known splicing variants.
- ISVASE identifies sequence variants for each splicing variant first, then identifies sequence variants for all related splicing variants (same junction start or end) for comparison analysis and statistical test.
- ISVASE identifies and judges sequence variants for both parts of junction separately, which can further distinguish the effect of sequence variants for different part of junction.
- ISVASE applies several stringent rule-depended filters and statistical filters in different steps.
- ISVASE considers the junction shift events and junction signals (5' ss and 3' ss) to remove the false splicing variants.
- ISVASE can use user provided DNA mutation and RNA editing data to designate the source type of sequence variants.
- ISVASE obtains flanking sequence of sequence variants for exonic splicing enhancer motif search.
- ISVASE can convert the default sequence variant file into ANNOVAR input format file for variant annotation.
- ISVASE use 8 figures to show the characteristics of sequence variants associated with splicing events.
Audience
Science/Research
Programming Language
Perl
This is an application that can also be fetched from https://sourceforge.net/projects/isvase/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.