ITriplet, a rule-based nucleic acid sequence motif finder.

ABSTRACT:

Background

With the advent of high throughput sequencing techniques, large amounts of sequencing data are readily available for analysis. Natural biological signals are intrinsically highly variable making their complete identification a computationally challenging problem. Many attempts in using statistical or combinatorial approaches have been made with great success in the past. However, identifying highly degenerate and long (>20 nucleotides) motifs still remains an unmet challenge as high degeneracy will diminish statistical significance of biological signals and increasing motif size will cause combinatorial explosion. In this report, we present a novel rule-based method that is focused on finding degenerate and long motifs. Our proposed method, named iTriplet, avoids costly

SUBMITTER: Ho ES 

PROVIDER: S-EPMC2784457 | biostudies-literature | 2009 Oct

REPOSITORIES: biostudies-literature