Work

RNApasta: a tool for analysis of RNA structural alignments

Year: 2010

Type: article

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.

Source: International Journal of Bioinformatics Research and Applications

DOI: 10.1504/ijbra.2010.038738

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

Institution: University of Georgia

Language: English

Topic: RNA and protein synthesis mechanisms

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

Funders: National Institutes of Health, National Institute of General Medical Sciences

Awards: G123820411, Searching Genomes for Non-Coding RNAs by Their Structure, G2755411256