CNEFinder: Finding conserved non-coding elements in genomes

Lorraine A.K. Ayad*, Solon P. Pissis, Dimitris Polychronopoulos

*Corresponding author for this work

Research output: Contribution to JournalArticleAcademicpeer-review


Motivation Conserved 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. Results We fill this gap by presenting CNEFinder; 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. CNEFinder 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 implementation Free software under the terms of the GNU GPL (

Original languageEnglish
Pages (from-to)i743-i747
Issue number17
Publication statusPublished - 1 Sept 2018
Externally publishedYes


Dive into the research topics of 'CNEFinder: Finding conserved non-coding elements in genomes'. Together they form a unique fingerprint.

Cite this