Title: RNApasta: a tool for analysis of RNA structural alignments

Authors: Russell L. Malmberg, Timothy I. Shaw, Liming Cai

Addresses: Department of Plant Biology, University of Georgia, Athens, GA 30602, USA; Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA. ' Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA. ' Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA; Department of Computer Science, University of Georgia, Athens, GA 30602, USA

Abstract: The study of RNA sequence structural alignments has become an important part of characterising noncoding RNAs. We developed RNApasta, a Java program with a graphical interface, to perform analysis and editing of RNA alignments. RNApasta can be used to generate statistics for modelling RNAs and to develop homogeneous subsets of alignments that contain variability. RNApasta includes several functions to characterise variation in stem and loop lengths, including phylogenetic analysis of this variation; as an example, we analyse variation in mir-31 pre-microRNA loop length variation, demonstrating that the sequences with longer loops had a single evolutionary origin.

Keywords: RNA structural alignment; alignment viewer; secondary structure; variation; evolution; RNA sequences; bioinformatics; Java; RNA modelling; RNA alignments.

DOI: 10.1504/IJBRA.2010.038738

International Journal of Bioinformatics Research and Applications, 2010 Vol.6 No.6, pp.571 - 583

Received: 11 Mar 2010
Accepted: 06 May 2010

Published online: 24 Feb 2011 *

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