KEC: unique sequence search by K-mer exclusion

Pavel Beran; Dagmar Stehlíková; Stephen P Cohen; Vladislav Čurn

doi:10.1093/bioinformatics/btab196

KEC: unique sequence search by K-mer exclusion

Bioinformatics. 2021 Oct 11;37(19):3349-3350. doi: 10.1093/bioinformatics/btab196.

Authors

Pavel Beran¹, Dagmar Stehlíková¹, Stephen P Cohen², Vladislav Čurn¹

Affiliations

¹ Department of Genetics and Agricultural Biotechnology, Biotechnological Centre, University of South Bohemia, Faculty of Agriculture, 37005 České Budějovice, Czech Republic.
² Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, USA.

PMID: 33755102
DOI: 10.1093/bioinformatics/btab196

Abstract

Summary: Searching for amino acid or nucleic acid sequences unique to one organism may be challenging depending on size of the available datasets. K-mer elimination by cross-reference (KEC) allows users to quickly and easily find unique sequences by providing target and non-target sequences. Due to its speed, it can be used for datasets of genomic size and can be run on desktop or laptop computers with modest specifications.

Availability and implementation: KEC is freely available for non-commercial purposes. Source code and executable binary files compiled for Linux, Mac and Windows can be downloaded from https://github.com/berybox/KEC.

Supplementary information: Supplementary data are available at Bioinformatics online.

Abstract

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