Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts.

ABSTRACT:

Motivation

The identity of cells and tissues is to a large degree governed by transcriptional regulation. A major part is accomplished by the combinatorial binding of transcription factors at regulatory sequences, such as enhancers. Even though binding of transcription factors is sequence-specific, estimating the sequence similarity of two functionally similar enhancers is very difficult. However, a similarity measure for regulatory sequences is crucial to detect and understand functional similarities between two enhancers and will facilitate large-scale analyses like clustering, prediction and classification of genome-wide datasets.

Results

We present the standardized alignment-free sequence similarity measure N2, a flexible framework that is defined for word neighbourhoods

SUBMITTER: Goke J 

PROVIDER: S-EPMC3289921 | biostudies-literature | 2012 Mar

REPOSITORIES: biostudies-literature