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Abstract
Fast Pairwise Structural RNA Alignments by Pruning of the Dynamical Programming Matrix
Highlights
Noncoding RNA genes and regulatory structures have been shown to be both highly abundant and highly diverse parts of the genome [1,2]
It has been shown that alignment of noncoding RNA (ncRNA) requires information about secondary structure when the sequence similarity is below 60% [7]
FOLDALIGN is an algorithm for making pairwise structural alignments of RNA sequences
Summary
Noncoding RNA (ncRNA) genes and regulatory structures have been shown to be both highly abundant and highly diverse parts of the genome [1,2]. Several papers about large-scale searches for vertebrate RNA genes or motifs using comparative genomics have been published [4,5,6]. These large-scale searches indicate that there are potentially many unknown structures still hidden in the genomes. It has been shown that alignment of ncRNAs requires information about secondary structure when the sequence similarity is below 60% [7]. Heuristics are needed before the algorithms for folding and aligning RNA sequences become fast enough to be useful
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