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.
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.
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.
Rests on the formalization of the difficulty of detecting splice sites as an optimization problem. ASPIC provides a minimal set of transcript isoforms explaining all alternative splice events occurring among the set of transcripts considered. It contains a module for detecting and scoring splice junctions by using quality measures. Its algorithm implements a novel methodology that optimizes the overall compatibility between genomic and transcript sequences.
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 secondary analysis of next-generation sequencing (NGS) data. DRAGEN uses a reconfigurable field-programmable gate array (FPGA) to provide hardware-accelerated implementations of secondary analysis pipeline algorithms, such as BCL conversion, compression, mapping, alignment, sorting, duplicate marking, and haplotype variant calling. This software can be leveraged as a blended hybrid of the onsite and Cloud solutions.
Detects synonymous regulatory elements (SREs) in vertebrate genomes. SynoR is based on conserved transcription factor binding sites (cTFBS) and performs genome scans for regulatory elements (REs) with shared biological activity. It offers possibility to users to extend the knowledge derived from a single gene’s regulatory genomic structure to the whole genome. It also can notice genes with synonymous regulation.
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.