An alignment-free method to identify candidate orthologous enhancers in multiple Drosophila genomes.

ABSTRACT:

Motivation

Evolutionarily conserved non-coding genomic sequences represent a potentially rich source for the discovery of gene regulatory region such as transcriptional enhancers. However, detecting orthologous enhancers using alignment-based methods in higher eukaryotic genomes is particularly challenging, as regulatory regions can undergo considerable sequence changes while maintaining their functionality.

Results

We have developed an alignment-free method which identifies conserved enhancers in multiple diverged species. Our method is based on similarity metrics between two sequences based on the co-occurrence of sequence patterns regardless of their order and orientation, thus tolerating sequence changes observed in non-coding evolution. We show that our method is highly

SUBMITTER: Arunachalam M 

PROVIDER: S-EPMC2922894 | biostudies-literature | 2010 Sep

REPOSITORIES: biostudies-literature