Motivation: Structured non-coding RNAs (ncRNAs) have a very important functional role in the cell. No distinctive general features common to all ncRNA have yet been discovered. This makes it difficult to design computational tools able to detect novel ncRNAs in the genomic sequence. Results: We devised an algorithm able to detect conserved secondary structures in both pairwise and multiple DNA sequence alignments with computational time proportional to the square of the sequence length. We implemented the algorithm for the case of pairwise and three-way alignments and tested it on ncRNAs obtained from public databases. On the test sets, the pairwise algorithm has a specificity greater than 97% with a sensitivity varying from 22.26% for Blast alignments to 56.35% for structural alignments. The three-way algorithm behaves similarly. Our algorithm is able to efficiently detect a conserved secondary structure in multiple alignments. Availability: The executable file, the code and a PDF file containing the instructions, as well as the test data sets can be requested free of charge from the authors (dibernardo@tigem.it) or from the website http://www.tigem.it/ research/dibernardo/default.htm Contact: dibernardo@tigem.it
['Diego di Bernardo', 'Thomas A. Down', 'Tim Hubbard']
ddbRNA: detection of conserved secondary structures in multiple alignments