+ Site Statistics
+ Search Articles
+ PDF Full Text Service
How our service works
Request PDF Full Text
+ Follow Us
Follow on Facebook
Follow on Twitter
Follow on LinkedIn
+ Subscribe to Site Feeds
Most Shared
PDF Full Text
+ Translate
+ Recently Requested

Alt Event Finder: a tool for extracting alternative splicing events from RNA-seq data

Alt Event Finder: a tool for extracting alternative splicing events from RNA-seq data

Bmc Genomics 13(Suppl. 8): S10

Alternative splicing increases proteome diversity by expressing multiple gene isoforms that often differ in function. Identifying alternative splicing events from RNA-seq experiments is important for understanding the diversity of transcripts and for investigating the regulation of splicing. We developed Alt Event Finder, a tool for identifying novel splicing events by using transcript annotation derived from genome-guided construction tools, such as Cufflinks and Scripture. With a proper combination of alignment and transcript reconstruction tools, Alt Event Finder is capable of identifying novel splicing events in the human genome. We further applied Alt Event Finder on a set of RNA-seq data from rat liver tissues, and identified dozens of novel cassette exon events whose splicing patterns changed after extensive alcohol exposure. Alt Event Finder is capable of identifying de novo splicing events from data-driven transcript annotation, and is a useful tool for studying splicing regulation.

Please choose payment method:

(PDF emailed within 0-6 h: $19.90)

Accession: 036682687

Download citation: RISBibTeXText

PMID: 23281921

DOI: 10.1186/1471-2164-13-s8-s10

Related references

Alternative Splicing Detection Tool-a novel PERL algorithm for sensitive detection of splicing events, based on next-generation sequencing data analysis. Annals of Translational Medicine 6(12): 244, 2018

Splicy: a web-based tool for the prediction of possible alternative splicing events from Affymetrix probeset data. Bmc Bioinformatics 8(Suppl. 1): S17, 2007

Human Splicing Finder: an online bioinformatics tool to predict splicing signals. Nucleic Acids Research 37(9): E67, 2009

ASGAL: aligning RNA-Seq data to a splicing graph to detect novel alternative splicing events. Bmc Bioinformatics 19(1): 444, 2018

Alternative splicing events is not a key event for gene expression regulation in uremia. Plos One 8(12): E82702, 2014

Identification of rare alternative splicing events in MS/MS data reveals a significant fraction of alternative translation initiation sites. Peerj 2: E673, 2014

KISSPLICE: de-novo calling alternative splicing events from RNA-seq data. Bmc Bioinformatics 13(Suppl. 6): S5, 2012

SplicingTypesAnno: annotating and quantifying alternative splicing events for RNA-Seq data. Computer Methods and Programs in Biomedicine 119(1): 53-62, 2015

SplAdder: identification, quantification and testing of alternative splicing events from RNA-Seq data. Bioinformatics 32(12): 1840-1847, 2017

Identifying differential alternative splicing events from RNA sequencing data using RNASeq-MATS. Methods in Molecular Biology 1038: 171-179, 2014

REMAS: a new regression model to identify alternative splicing events from exon array data. Bmc Bioinformatics 10(Suppl. 1): S18, 2009

Identification of potentially new bifunctional RNA based on genome-wide data-mining of alternative splicing events. Biochimie 93(11): 2024-2027, 2012

Prognostic Signature of Alternative Splicing Events in Bladder Urothelial Carcinoma Based on Spliceseq Data from 317 Cases. Cellular Physiology and Biochemistry 48(3): 1355-1368, 2018

Strategies for identifying RNA splicing regulatory motifs and predicting alternative splicing events. Plos Computational Biology 4(1): E21, 2008

Strategies for identifying RNA splicing regulatory motifs and predicting alternative splicing events. PLoS Computational Biology 4(1): e21, 2008