Fast online and index-based algorithms for approximate search of RNA sequence-structure patterns.

ABSTRACT:

Background

It is well known that the search for homologous RNAs is more effective if both sequence and structure information is incorporated into the search. However, current tools for searching with RNA sequence-structure patterns cannot fully handle mutations occurring on both these levels or are simply not fast enough for searching large sequence databases because of the high computational costs of the underlying sequence-structure alignment problem.

Results

We present new fast index-based and online algorithms for approximate matching of RNA sequence-structure patterns supporting a full set of edit operations on single bases and base pairs. Our methods efficiently compute semi-global alignments of structural RNA patterns and substrings of the target sequence whose costs

SUBMITTER: Meyer F 

PROVIDER: S-EPMC3765529 | biostudies-literature | 2013 Jul

REPOSITORIES: biostudies-literature