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Alternative polyadenylation identification 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, global cancer APA studies are very limited.

Source text:
(Xia et al., 2014) Dynamic analyses of alternative polyadenylation from RNA-seq reveal a 3'-UTR landscape across seven tumour types. Nat Commun.

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DaPars / Dynamic analysis of Alternative PolyAdenylation from RNA-seq
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, uses a regression model to infer the exact location of the proximal APA site after correcting the potential RNA-seq non-uniformity bias along gene body, detects statistically significant dynamic APAs and has the potential to detect >2 dynamic APA events.
QAPA / Quantification of APA
Deduces alternative polyadenylation (APA) from conventional RNA-seq data. QAPA uses conventional RNA-seq data to infer poly(A) site selection and alternative 3′ UTR usage. The software employs estimation of alternative 3′ untranslated region (UTR) expression in combination with an expanded resource of annotated poly(A) sites to demarcate UTR sequences that are specifically affected by APA. It facilitates the systematic discovery and characterization of APA across diverse physiologically normal and disease conditions.
3USS / 3' Utr Sequence Seeker
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 option that is not available in standard RNA-seq data analysis procedures. The tool reports as putative novel the 3'UTRs not annotated in available databases. Furthermore, if data from two related samples are uploaded, common and specific alternative 3'UTRs are identified and reported by the server.
TAPAS / Tool for Alternative Polyadenylation Site Analysis
Identifies alternative polyadenylation (APA) sites from RNA-Seq data. TAPAS is a standalone application mainly based on the Pruned Exact Linear Time (PELT) method. The application supplies three main features: (i) APA detection; (ii) determining genes with differentially expressed APA sites and (iii) and those with shortening/lengthening events. The software is able to consider 3′ untranslated regions (UTRs) including intronic regions.
roar / Ratio Of A Ratio
Identifies preferential usage of alternative polyadenylation (APA) sites, comparing two biological conditions, starting from known alternative sites and alignments obtained from standard RNA-seq experiments. roar approach is based on Fisher test to detect disequilibriums in the number of reads falling over the 3’UTRs when comparing two biological conditions. Counts and fragments lengths are used to calculate the prevalence of the short isoform over the long one in both conditions, therefore the ratio of these ratios represents the relative “shortening” (or lengthening) in one condition with respect to the other.
RNAelements
Obsolete
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) analysis. It aims to identify motifs containing secondary structural information important for RBP binding from recent CLIP-seq or RIP-chip data for RBPs. The RNAelements can be used to identify binding motifs with a higher percentage of matches to the known RBP datasets. As only a few large-scale datasets are available for RBPs, this server is thus limited for those RBPs.
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