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ddbRNA: detection of conserved secondary structures in multiple alignments.

Authors
Type
Published Article
Journal
Bioinformatics (Oxford, England)
Publication Date
Volume
19
Issue
13
Pages
1606–1611
Identifiers
PMID: 12967955
Source
Medline
License
Unknown

Abstract

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.

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