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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 (Smith and Valcarcel, 2000; Tress et al., 2007). The…
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APPRIS
Web

APPRIS

The main goal of developing the APPRIS WebServer and WebServices is to allow…

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…

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rPGA
Desktop

rPGA RNA-seq Personal Genome-alignment Analyzer

Allows users to discover hidden splice junctions by mapping personal RNA-seq…

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…

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FSOM
Desktop

FSOM

A computational technique for the study of stable methylation patterns which is…

A computational technique for the study of stable methylation patterns which is a crucial piece of the puzzle in the attempt to understand the influence of DNA methylation on the regulation of…

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expressRNA
Web

expressRNA

Processes 3’ mRNA sequencing data. expressRNA classifies the sites where…

Processes 3’ mRNA sequencing data. expressRNA classifies the sites where cleavage and polyadenylation take place. It is able to identify the differentially regulated poly(A) sites. This tool…

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iSS-PseDNC
Algorithm

iSS-PseDNC Identifying Splice site Pseudo DiNucleotide Composition

Allows users to identify splice sites. iSS-PseDNC is useful for splice site…

Allows users to identify splice sites. iSS-PseDNC is useful for splice site recognitions and is a predictor that uses a "pseudo dinucleotide composition” (PseDNC). This PseDNC serves to…

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PULSE
Desktop

PULSE

A semi-supervised learning algorithm, positive unlabeled learning for splicing…

A semi-supervised learning algorithm, positive unlabeled learning for splicing elucidation, which uses 48 features spanning various categories. PULSE predicts ∼32% of isoforms as stably folded.…

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DeepCode
Algorithm

DeepCode

Allows prediction of alternative splicing (AS) patterns. DeepCode can serve for…

Allows prediction of alternative splicing (AS) patterns. DeepCode can serve for human embryonic stem cell (hESC) differentiation by integrating heterogeneous features of genomic sequences. It is…

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TAPAS
Desktop

TAPAS

Helps in isoform target prioritisation and experimental design. Given the…

Helps in isoform target prioritisation and experimental design. Given the biological and experimental noise associated with alternative splicing, TAPAS prioritises those splicing events that show a…

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WebScipio
Web

WebScipio

Allows predicting mutually exclusive spliced exons and tandemly arrayed gene…

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…

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TassDB
Dataset

TassDB TAndem Splice Site DataBase

Stores extensive data about alternative splice events at donors and acceptors,…

Stores extensive data about alternative splice events at donors and acceptors, both confirmed and unconfirmed cases. TassDB offers a user-friendly interface to search for specific genes or for genes…

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CoSREM
Desktop

CoSREM Combinatorial SRE Miner

A graph mining algorithm to discover combinatorial splicing regulatory elements…

A graph mining algorithm to discover combinatorial splicing regulatory elements (SREs) in human exons. Our model does not assume a fixed length of SREs and incorporates experimental evidence as well…

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AS-EAST
Web

AS-EAST Alternative Splicing Effects ASsessment Tools

An online tool for the functional annotation of putative proteins encoded by…

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…

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SNPSplicer
Desktop

SNPSplicer

A Windows program for the systematic analysis of SNP-dependent splicing in…

A Windows program for the systematic analysis of SNP-dependent splicing in genotyped cDNAs. This methodology may help in the functional annotation of SNPs in a more high-throughput fashion.

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GSReg
Desktop

GSReg Gene Set Regulation

Permits to recognize Alternative Splicing Events (ASE). GSReg is based on the…

Permits to recognize Alternative Splicing Events (ASE). GSReg is based on the variability of expressions. It considers the ordering of the expressions within the pathway. The tool can perform the…

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neuronvar
Desktop

neuronvar

Allows to study RNA Isoform Variability in Neurons.

Allows to study RNA Isoform Variability in Neurons.

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ASpipe
Desktop

ASpipe Alternative Splicing Pipeline

Allows to create GeneSeqer/Genomic Mapping and Alignment Program (GMAP)…

Allows to create GeneSeqer/Genomic Mapping and Alignment Program (GMAP) alignments. ASpipe enables to identify alternative splicing (AS) events from the alignments.

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outrigger
Desktop

outrigger

Uses junction reads from RNA seq data, and a graph database to create a de novo…

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…

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ASPIC
Web

ASPIC Alternative Splicing PredICtion

Rests on the formalization of the difficulty of detecting splice sites as an…

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…

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MAISTAS
Web

MAISTAS Modeling and Assessment of ISoforms Through Automated Server

A fully automatic pipeline aimed at building and assessing three-dimensional…

A fully automatic pipeline aimed at building and assessing three-dimensional models for alternative splicing isoforms. MAISTAS, given a gene or a protein, retrieves and analyses all its annotated…

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