RILogo: visualizing RNA-RNA interactions.
Bioinformatics
; 28(19): 2523-6, 2012 Oct 01.
Article
en En
| MEDLINE
| ID: mdl-22826541
ABSTRACT
SUMMARY:
With the increasing amount of newly discovered non-coding RNAs, the interactions between RNA molecules become an increasingly important aspect for characterizing their functionality. Many computational tools have been developed to predict the formation of duplexes between two RNAs, either based on single sequences or alignments of homologous sequences. Here, we present RILogo, a program to visualize inter- and intramolecular base pairing between two RNA molecules. The input for RILogo is a pair of structure-annotated sequences or alignments. In the latter case, RILogo displays the alignments in the form of sequence logos, including the mutual information of base paired columns. We also introduce two novel mutual information based measures that weigh the covariance information by the evolutionary distances of the aligned sequences. We show that the new measures have an increased accuracy compared with previous mutual information measures. AVAILABILITY AND IMPLEMENTATION RILogo is freely available as a stand-alone program and is accessible via a web server at http//rth.dk/resources/rilogo. CONTACT pmenzel@gmail.com SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Banco de datos:
MEDLINE
Asunto principal:
Programas Informáticos
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Alineación de Secuencia
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Emparejamiento Base
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ARN no Traducido
Idioma:
En
Revista:
Bioinformatics
Asunto de la revista:
INFORMATICA MEDICA
Año:
2012
Tipo del documento:
Article
País de afiliación:
Dinamarca