RILogo: visualising RNA-RNA interactions

TY - JOUR

T1 - RILogo

T2 - visualising RNA-RNA interactions

AU - Menzel, Karl Peter

AU - Seemann, Ernst Stefan

AU - Gorodkin, Jan

PY - 2012/10

Y1 - 2012/10

N2 - 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.

AB - 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.

U2 - 10.1093/bioinformatics/bts461

DO - 10.1093/bioinformatics/bts461

M3 - Journal article

C2 - 22826541

SN - 1367-4803

VL - 28

SP - 2523

EP - 2526

JO - Bioinformatics

JF - Bioinformatics

IS - 19

ER -