3USS: a web server for detecting alternative 3'UTRs from RNA-seq experiments.

Handle URI:
http://hdl.handle.net/10754/596754
Title:
3USS: a web server for detecting alternative 3'UTRs from RNA-seq experiments.
Authors:
Le Pera, Loredana; Mazzapioda, Mariagiovanna; Tramontano, Anna
Abstract:
Protein-coding genes with multiple alternative polyadenylation sites can generate mRNA 3'UTR sequences of different lengths, thereby causing the loss or gain of regulatory elements, which can affect stability, localization and translation efficiency. 3USS is 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.3USS is freely available at http://www.biocomputing.it/3uss_server.
Citation:
Le Pera L, Mazzapioda M, Tramontano A (2015) 3USS: a web server for detecting alternative 3’UTRs from RNA-seq experiments. Bioinformatics 31: 1845–1847. Available: http://dx.doi.org/10.1093/bioinformatics/btv035.
Publisher:
Oxford University Press (OUP)
Journal:
Bioinformatics
KAUST Grant Number:
KUK-I1-012-43
Issue Date:
22-Jan-2015
DOI:
10.1093/bioinformatics/btv035
PubMed ID:
25617413
PubMed Central ID:
PMC4443675
Type:
Article
ISSN:
1367-4803; 1460-2059
Sponsors:
This project was supported by KAUST [Grant Number KUK-I1-012-43], PRIN 20108XYHJS and Epigenomics Flagship Project—EPIGEN. Funding for open access charge: KAUST.
Appears in Collections:
Publications Acknowledging KAUST Support

Full metadata record

DC FieldValue Language
dc.contributor.authorLe Pera, Loredanaen
dc.contributor.authorMazzapioda, Mariagiovannaen
dc.contributor.authorTramontano, Annaen
dc.date.accessioned2016-02-21T08:49:40Zen
dc.date.available2016-02-21T08:49:40Zen
dc.date.issued2015-01-22en
dc.identifier.citationLe Pera L, Mazzapioda M, Tramontano A (2015) 3USS: a web server for detecting alternative 3’UTRs from RNA-seq experiments. Bioinformatics 31: 1845–1847. Available: http://dx.doi.org/10.1093/bioinformatics/btv035.en
dc.identifier.issn1367-4803en
dc.identifier.issn1460-2059en
dc.identifier.pmid25617413en
dc.identifier.doi10.1093/bioinformatics/btv035en
dc.identifier.urihttp://hdl.handle.net/10754/596754en
dc.description.abstractProtein-coding genes with multiple alternative polyadenylation sites can generate mRNA 3'UTR sequences of different lengths, thereby causing the loss or gain of regulatory elements, which can affect stability, localization and translation efficiency. 3USS is 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.3USS is freely available at http://www.biocomputing.it/3uss_server.en
dc.description.sponsorshipThis project was supported by KAUST [Grant Number KUK-I1-012-43], PRIN 20108XYHJS and Epigenomics Flagship Project—EPIGEN. Funding for open access charge: KAUST.en
dc.publisherOxford University Press (OUP)en
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.comen
dc.rights.urihttp://creativecommons.org/licenses/by-nc/4.0/en
dc.subject.mesh3' Untranslated Regionsen
dc.subject.meshGene Expression Profilingen
dc.subject.meshSequence Analysis, RNAen
dc.subject.meshSoftwareen
dc.title3USS: a web server for detecting alternative 3'UTRs from RNA-seq experiments.en
dc.typeArticleen
dc.identifier.journalBioinformaticsen
dc.identifier.pmcidPMC4443675en
dc.contributor.institutionCenter for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy, Department of Physics, Sapienza University, Rome, Italy and Istituto Pasteur - Fondazione Cenci Bolognetti, Sapienza University, Rome, Italy Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy, Department of Physics, Sapienza University, Rome, Italy and Istituto Pasteur - Fondazione Cenci Bolognetti, Sapienza University, Rome, Italy.en
dc.contributor.institutionCenter for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy, Department of Physics, Sapienza University, Rome, Italy and Istituto Pasteur - Fondazione Cenci Bolognetti, Sapienza University, Rome, Italy.en
dc.contributor.institutionCenter for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy, Department of Physics, Sapienza University, Rome, Italy and Istituto Pasteur - Fondazione Cenci Bolognetti, Sapienza University, Rome, Italy Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy, Department of Physics, Sapienza University, Rome, Italy and Istituto Pasteur - Fondazione Cenci Bolognetti, Sapienza University, Rome, Italy Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy, Department of Physics, Sapienza University, Rome, Italy and Istituto Pasteur - Fondazione Cenci Bolognetti, Sapienza University, Rome, Italy.en
kaust.grant.numberKUK-I1-012-43en

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