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

Loredana Le Pera; Mariagiovanna Mazzapioda; Anna Tramontano

doi:10.1093/bioinformatics/btv035

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

Loredana Le Pera, Mariagiovanna Mazzapioda, Anna Tramontano

Research output: Contribution to journal › Article › peer-review

26 Scopus citations

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.

Original language	English (US)
Pages (from-to)	1845-1847
Number of pages	3
Journal	Bioinformatics
Volume	31
Issue number	11
DOIs	https://doi.org/10.1093/bioinformatics/btv035
State	Published - Jan 22 2015
Externally published	Yes

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01
Acknowledged KAUST grant number(s): KUK-I1-012-43
Acknowledgements: 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.
This publication acknowledges KAUST support, but has no KAUST affiliated authors.

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10.1093/bioinformatics/btv035

https://repository.kaust.edu.sa/bitstream/10754/596754/1/PMC4443675.pdf

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@article{9341911958b14cecb86fc848f7956842,

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

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.",

author = "{Le Pera}, Loredana and Mariagiovanna Mazzapioda and Anna Tramontano",

note = "KAUST Repository Item: Exported on 2020-10-01 Acknowledged KAUST grant number(s): KUK-I1-012-43 Acknowledgements: 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. This publication acknowledges KAUST support, but has no KAUST affiliated authors.",

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doi = "10.1093/bioinformatics/btv035",

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AU - Mazzapioda, Mariagiovanna

AU - Tramontano, Anna

N1 - KAUST Repository Item: Exported on 2020-10-01 Acknowledged KAUST grant number(s): KUK-I1-012-43 Acknowledgements: 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. This publication acknowledges KAUST support, but has no KAUST affiliated authors.

PY - 2015/1/22

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N2 - 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.

AB - 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.

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JO - Bioinformatics

JF - Bioinformatics

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ER -

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

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