Genome-scale NCRNA homology search using a Hamming distance-based filtration strategy.

ABSTRACT:

Background

NCRNAs (noncoding RNAs) play important roles in many biological processes. Existing genome-scale ncRNA search tools identify ncRNAs in local sequence alignments generated by conventional sequence comparison methods. However, some types of ncRNA lack strong sequence conservation and tend to be missed or mis-aligned by conventional sequence comparison.

Results

In this paper, we propose an ncRNA identification framework that is complementary to existing sequence comparison tools. By integrating a filtration step based on Hamming distance and ncRNA alignment programs such as FOLDALIGN or PLAST-ncRNA, the proposed ncRNA search framework can identify ncRNAs that lack strong sequence conservation. In addition, as the ratio of transition and transversion mutation is often

SUBMITTER: Sun Y 

PROVIDER: S-EPMC3311100 | biostudies-literature | 2012 Mar

REPOSITORIES: biostudies-literature