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).
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.
An application written in python that detects and visualizes alternative splicing events using spliced alignments. Sircah takes as input transcript models in the GFF3 format allowing the user the flexibility to choose the sources of evidence for the use in detecting alternative transcription.
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