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Alternative polyadenylation detection software tools | RNA sequencing data analysis

Alternative polyadenylation (APA) is a pervasive mechanism in the regulation of most human genes, and its implication in diseases including cancer is only beginning to be appreciated. Since conventional APA profiling has not been widely adopted,…
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apa
Desktop

apa Alternative PolyAdenylation analysis

Allows users to process and analyze 3'-end sequencing data. apa aims to…

Allows users to process and analyze 3'-end sequencing data. apa aims to permit the study of alternative polyadenylation. It marks and annotates the differentially regulated poly(A) sites, and…

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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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roar
Desktop

roar Ratio Of A Ratio

Identifies preferential usage of alternative polyadenylation (APA) sites,…

Identifies preferential usage of alternative polyadenylation (APA) sites, comparing two biological conditions, starting from known alternative sites and alignments obtained from standard RNA-seq…

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DaPars
Desktop

DaPars Dynamic analysis of Alternative PolyAdenylation from RNA-seq

Performs de novo identification and quantification of dynamic APA events…

Performs de novo identification and quantification of dynamic APA events between two conditions, regardless of any prior APA annotation. DaPars identifies a distal polyA site based on RNA-seq data,…

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ExUTR
Desktop

ExUTR

Allows users to perform 3′-UTR landscape prediction from RNA-Seq experiments.…

Allows users to perform 3′-UTR landscape prediction from RNA-Seq experiments. ExUTR is a standalone software based on a genome-wide approach for detecting 3′-UTR candidates from both…

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3USS
Web

3USS 3' Utr Sequence Seeker

A web-server developed with the aim of giving experimentalists the possibility…

A web-server developed with the aim of giving experimentalists the possibility to automatically identify alternative 3'UTRs (shorter or longer with respect to a reference transcriptome), an…

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IsoSCM
Desktop

IsoSCM Isoform Structural Change Model

A method for transcript assembly that incorporates change-point analysis to…

A method for transcript assembly that incorporates change-point analysis to improve the 3' UTR annotation process. IsoSCM will facilitate future efforts for 3' UTR annotation and…

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PHMM
Desktop

PHMM Poisson Hidden Markov Model

Identifies shortening of 3′ untranslated regions (UTRs). PHMM is based on a…

Identifies shortening of 3′ untranslated regions (UTRs). PHMM is based on a Poisson hidden Markov model (PHMM) and was compared with a probabilistic approach to quantification of transcripts at the…

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GETUTR
Desktop

GETUTR Global Estimation of the 3' UTR landscape based on RNA sequencing

Estimates the 3′ UTR landscape from high-throughput RNA sequencing. GETUTR…

Estimates the 3′ UTR landscape from high-throughput RNA sequencing. GETUTR provides fast and low complexity algorithms to process large-scale RNA-seq data. It leads to a better understanding of UTR…

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maps3end
Desktop

maps3end

A simple and cost-effective 3'-end RNA-seq technology. This package…

A simple and cost-effective 3'-end RNA-seq technology. This package provides Python scripts for some basic tasks on the MAPS sequencing data from Illumina sequencer.

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ChangePoint
Desktop

ChangePoint

A change-point model based on a likelihood ratio test for detecting 3'UTR…

A change-point model based on a likelihood ratio test for detecting 3'UTR switching. A directional testing procedure is developed for identifying dramatic shortening or lengthening events in…

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CLEAT
Desktop

CLEAT CLEavage site Analysis of Transcriptomes

Characterizes 3’ untranslated regions (UTRs) in assembled RNA-seq data…

Characterizes 3’ untranslated regions (UTRs) in assembled RNA-seq data through direct observation of poly(A) tails. KLEAT employes several evidence types within RNA-seq reads to analyze the…

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pybio
Desktop

pybio

Permits users to proceed to basic genomics operations. pybio offers motif…

Permits users to proceed to basic genomics operations. pybio offers motif sequence searches functions. It can classify alternative polyadenylation site-pair.

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FindTail
Desktop

FindTail

Detects all perfect poly(A) tracts (or homopolymers) in a sequence. Starting…

Detects all perfect poly(A) tracts (or homopolymers) in a sequence. Starting with the first tract, FindTail then determines whether the downstream tracts can be merged to form a longer poly(A)…

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RNAelements
Web

RNAelements

Predicts RNA bindings in the UTR regions. RNAelements is a computational…

Predicts RNA bindings in the UTR regions. RNAelements is a computational pipeline using covariance model from known RNA binding protein (RBP) targets acquired by RNA Immunoprecipitation (RIP)…

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