Exon skipping identification software tools | RNA sequencing data analysis
Considering that more than 90% of the human multi-exon genes have been found to undergo alternative splicing (AS), exon-skipping could be one of the most important ways to steer transcriptional regulation. RNA-seq enables better characterization and quantification of individual transcriptomes because it can detect both gene expression and alternative splicing AS. Exon-skipping is the most common AS mechanism known in mammals, and is a major contributor to protein diversity in mammals. Exon-skipping results in the loss of an exon in the alternatively spliced mRNA.
An easy-to-use application for microarray, RNA-Seq and metabolomics analysis. For splicing sensitive platforms (RNA-Seq or Affymetrix Exon, Gene and Junction arrays), AltAnalyze will assess alternative exon (known and novel) expression along protein isoforms, domain composition and microRNA targeting. In addition to splicing-sensitive platforms, AltAnalyze provides comprehensive methods for the analysis of other data (RMA summarization, batch-effect removal, QC, statistics, annotation, clustering, network creation, lineage characterization, alternative exon visualization, gene-set enrichment and more).
Allows identification, extraction and displaying of complex alternative splicing (AS) events from annotated genes. AStalavista is an alternative splicing transcriptional landscape visualization tool for investigating and comparing types and distributions of the different AS events found in whole genome annotations and user provided gene sets. The software enables identification of arbitrarily complex combinations of hitherto described AS events, either visually or by representation in a univocal notation system. It can be used if the sequencing/annotation process has not been completed.
Assists in discovering alternative splicing (AS) events in transcripts predicted from RNA-seq data and in comparing them across multiple conditions. ASprofile is a program that can analyze all pairs of transcripts in the sixteen tissues to determine exons included in one transcript and skipped in the other. To realize these operations, this software is composed of several tools: “extract-as”; “extract-as-fpkm”; and “collect-fpkm”.
Sorts alternative splicing (AS) and discovers coding potential. spliceR simplifies downstream sequence analysis by allowing annotation of genomic coordinates of the differentially spliced elements. It is able to detect coding potential of transcripts, determines untranslated region (UTR) and open reading frame (ORF) lengths and predicts whether transcripts are nonsense mediated decay (NMD)-sensitive based on compatible annotated start codon positions and their downstream ORF.
Investigates splice junctions and alternative splicing (AS) events from RNA-Seq data. SplicingViewer provides a platform dedicated to the visualization of AS patterns. The software first aligns short reads to reference genome, then detect of candidate splice junctions, and, lastly align unmapped short reads to splice junctions. It also displays genome mapping and junction mapping reads.
Allows users to generate splicing event annotations from RNA-seq data. Alt Event Finder is a flexible standalone software, based on a data-driven approach, that started from reconstructed map of transcripts and isoforms from RNA-seq experiments to determine the potential alternative events and identify unknown cassette exon. Nevertheless, the power of the program depends on the sequencing depth.
Detects de novo exon-skipping events directly from raw RNA-seq data without prior knowledge of gene-annotation information. First, we build a splicing-site-linking graph from splicing-aware aligned reads using a greedy algorithm. We then iteratively scan this linking graph to obtain those patterns conforming to skipping events. Finally, we apply the MISO model to calculate the ratio of skipping versus inclusion isoforms and determine which is the dominant isoform.