CNEFinder: finding conserved non-coding elements in genomes.

Lorraine A K Ayad,Solon P Pissis,Dimitris Polychronopoulos

doi:10.1093/bioinformatics/bty601

Lorraine A K Ayad, Solon P Pissis + Show 1 more

Open Access

https://doi.org/10.1093/bioinformatics/bty601

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Abstract

MotivationConserved non-coding elements (CNEs) represent an enigmatic class of genomic elements which, despite being extremely conserved across evolution, do not encode for proteins. Their functions are still largely unknown. Thus, there exists a need to systematically investigate their roles in genomes. Towards this direction, identifying sets of CNEs in a wide range of organisms is an important first step. Currently, there are no tools published in the literature for systematically identifying CNEs in genomes.ResultsWe fill this gap by presenting ; a tool for identifying CNEs between two given DNA sequences with user-defined criteria. The results presented here show the tool’s ability of identifying CNEs accurately and efficiently. is based on a k-mer technique for computing maximal exact matches. The tool thus does not require or compute whole-genome alignments or indexes, such as the suffix array or the Burrows Wheeler Transform (BWT), which makes it flexible to use on a wide scale.Availability and implementationFree software under the terms of the GNU GPL (https://github.com/lorrainea/CNEFinder).

Highlights

IntroductionConserved non-coding elements (CNEs) are a pervasive class of elements that are usually identified by inspecting whole-genome alignments between two or more genomes
The tool does not require or compute whole-genome alignments or indexes, such as the suffix array or the Burrows Wheeler Transform (BWT), which makes it flexible to use on a wide scale
Conserved non-coding elements (CNEs) are a pervasive class of elements that are usually identified by inspecting whole-genome alignments between two or more genomes

Summary

Introduction

Conserved non-coding elements (CNEs) are a pervasive class of elements that are usually identified by inspecting whole-genome alignments between two or more genomes. CNEs can be extremely conserved across evolution, yet they do not encode for proteins. Some of these elements play roles in the development of multicellular organisms acting as enhancers (Aparicio et al, 1995). They can be referred to in the literature with different names (UCEs, UCNEs, CNS, to name a few), the prevailing view is that these sets of elements are largely overlapping, with their genesis, functions and evolutionary dynamics being largely unknown. CNE identification methods may be classified into two major categories: alignment-based and alignment-free methods

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