RNA structure framework: automated transcriptome-wide reconstruction of RNA secondary structures from high-throughput structure probing data.
Bioinformatics
; 32(3): 459-61, 2016 Feb 01.
Article
em En
| MEDLINE
| ID: mdl-26487736
ABSTRACT
SUMMARY:
The rapidly increasing number of discovered non-coding RNAs makes the understanding of their structure a key feature toward a deeper comprehension of gene expression regulation. Various enzymatic- and chemically- based approaches have been recently developed to allow whole-genome studies of RNA secondary structures. Several methods have been recently presented that allow high-throughput RNA structure probing (CIRS-seq, Structure-seq, SHAPE-seq, PARS, etc.) and unbiased structural inference of residues within RNAs in their native conformation. We here present an analysis toolkit, named RNA Structure Framework (RSF), which allows fast and fully-automated analysis of high-throughput structure probing data, from data pre-processing to whole-transcriptome RNA structure inference. AVAILABILITY AND IMPLEMENTATION RSF is written in Perl and is freely available under the GPLv3 license from http//rsf.hugef-research.org. CONTACT salvatore.oliviero@hugef-torino.org SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
RNA
/
Genoma Humano
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Análise de Sequência de RNA
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Biologia Computacional
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Transcriptoma
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Conformação de Ácido Nucleico
Limite:
Humans
Idioma:
En
Revista:
Bioinformatics
Assunto da revista:
INFORMATICA MEDICA
Ano de publicação:
2016
Tipo de documento:
Article
País de afiliação:
Itália