RScan: fast searching structural similarities for structured RNAs in large databases.

ABSTRACT:

Background

Many RNAs have evolutionarily conserved secondary structures instead of primary sequences. Recently, there are an increasing number of methods being developed with focus on the structural alignments for finding conserved secondary structures as well as common structural motifs in pair-wise or multiple sequences. A challenging task is to search similar structures quickly for structured RNA sequences in large genomic databases since existing methods are too slow to be used in large databases.

Results

An implementation of a fast structural alignment algorithm, RScan, is proposed to fulfill the task. RScan is developed by levering the advantages of both hashing algorithms and local alignment algorithms. In our experiment, on the average, the times for searching a tRNA

SUBMITTER: Xue C 

PROVIDER: S-EPMC1949409 | biostudies-literature | 2007 Jul

REPOSITORIES: biostudies-literature