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.
An online tool for the functional annotation of putative proteins encoded by transcripts generated by alternative splicing (AS). When provided with a transcript sequence, AS-EAST identifies regions altered by AS events in the putative protein sequence encoded by the transcript. Users can evaluate the predicted function of the putative protein by inspecting whether functional domains are included in the altered regions. Moreover, users can infer the loss of inter-molecular interactions in the protein network according to whether the AS events affect interaction residues observed in the 3D structure of the reference isoform. The information obtained from AS-EAST will help to design experimental analyses for the functional significance of novel splice isoforms.
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 predicting mutually exclusive spliced exons and tandemly arrayed gene duplicates. The obtained gene structures are illustrated in graphical schemes and can be analysed down to the nucleotide level. The set of eukaryotic genomes available at the WebScipio server is updated on a daily basis. WebScipio has a user-friendly web interface.
Allows users to predict performance on Arabidopsis thaliana and human sequences. SpliceMachine can be trained by users on their own data, and can perform a computationally annotation. Its interface permits users to obtain biological knowledge extracted from their data. Its approach employs linear support vector machines (LSVM) to compute a linear classification boundary between actual and pseudo splice sites.
Enables users to analyze pathways based on the variability of the expression of sets of genes that are targets of those pathways. GSReg is an R package that also enables the detection of alternative splicing events. It implements: (1) DIRAC, for calculating a measure of variability of the ordering of the expression of genes in a pathway for specific phenotype, (2) the alternative EVA statistic, and (3) SEVA for modelling of increased heterogeneity of splice variant usage between conditions.
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