Alternative splicing annotation software tools | RNA modification data analysis
The alternative splicing of messenger RNA generates a range of mature RNA transcripts, which if translated into stable proteins, would greatly enrich the repertoire of cellular functions. The functional annotation of these alternative isoforms presents a serious challenge, not least because of the sheer quantity of genomic data that is being generated by genome annotation projects.
The main goal of developing the APPRIS WebServer and WebServices is to allow users to annotate splice isoforms and select a principal isoform for vertebrate genome species beyond those that are annotated in the APPRIS Database, to annotate genes and variants that are missing from the APPRIS Database, and to annotate their experimental results with existing annotations. The APPRIS WebServer has been designed to be used for the comparison of splice isoform annotations for individual genes, while the APPRIS WebServices have been created to allow access to the APPRIS Database and to run an automatic version of the APPRIS server, using REST architecture to be portable, modular and flexible in the automation of programmatic scripts.
Allows users to discover hidden splice junctions by mapping personal RNA-seq data to the matching personal genome sequence. rPGA personalizes the reference genome according to an individual’s single nucleotide polymorphisms (SNPs) and then maps the individual’s transcriptome to the corresponding personal genome, and discovers novel splice variants specific to the individual. This software was applied to analyze RNA-seq data from individuals with whole-genome genotype data in the 1000 Genomes project.
Uses junction reads from RNA seq data, and a graph database to create a de novo alternative splicing annotation with a graph database. Outrigger is a Python package and an RNA-seq analysis software that quantify percent spliced-in (Psi) of the events. It finds novel splicing events, including novel exons and was developed to help user to be confident in alternative exon inclusion calculations. It is recommended to use the Anaconda Python Distribution and creates an environment to install outrigger.
Analyzes double traces. Trace Recalling allows users to deconvolute double traces resulting from simultaneously sequencing two DNA templates. The software works calling either one or two bases at each position in a double trace. It can find alternate splices in single-pass reads of reverse transcriptase-polymerase chain reaction (RT–PCR) products. Trace Recalling can be used to screen for multiple insertion sites in a random insertional mutagenesis library.
Predicts transcripts human mRNA and mouse protein sequence alignments. Exogean enables prediction of several alternative transcripts per gene. It can be useful for annotation of eukaryote protein coding genes based on alignments with proteins from a different species and/or mRNAs from the same species. This tool produces information on each predicted gene and transcript that summarizes their structure, the evidence used, the problems and conflicts encountered and the solutions applied.
You can access more results by creating a free plan account or unlimited content via a premium account.