{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,15]],"date-time":"2026-04-15T00:18:21Z","timestamp":1776212301782,"version":"3.50.1"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2020,4,4]],"date-time":"2020-04-04T00:00:00Z","timestamp":1585958400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"US National Institutes of Health","doi-asserted-by":"crossref","award":["R35-GM130151"],"award-info":[{"award-number":["R35-GM130151"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000288","name":"Royal Society","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000288","id-type":"DOI","asserted-by":"publisher"}]},{"name":"international exchange schema","award":["IE161405"],"award-info":[{"award-number":["IE161405"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Computing the uniqueness of k-mers for each position of a genome while allowing for up to e mismatches is computationally challenging. However, it is crucial for many biological applications such as the design of guide RNA for CRISPR experiments. More formally, the uniqueness or (k, e)-mappability can be described for every position as the reciprocal value of how often this k-mer occurs approximately in the genome, i.e. with up to e mismatches.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We present a fast method GenMap to compute the (k, e)-mappability. We extend the mappability algorithm, such that it can also be computed across multiple genomes where a k-mer occurrence is only counted once per genome. This allows for the computation of marker sequences or finding candidates for probe design by identifying approximate k-mers that are unique to a genome or that are present in all genomes. GenMap supports different formats such as binary output, wig and bed files as well as csv files to export the location of all approximate k-mers for each genomic position.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>GenMap can be installed via bioconda. Binaries and C++ source code are available on https:\/\/github.com\/cpockrandt\/genmap.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa222","type":"journal-article","created":{"date-parts":[[2020,3,31]],"date-time":"2020-03-31T15:21:14Z","timestamp":1585668074000},"page":"3687-3692","source":"Crossref","is-referenced-by-count":210,"title":["GenMap: ultra-fast computation of genome mappability"],"prefix":"10.1093","volume":"36","author":[{"given":"Christopher","family":"Pockrandt","sequence":"first","affiliation":[{"name":"Center for Computational Biology , School of Medicine"},{"name":"Department of Biomedical Engineering , Johns Hopkins University, Baltimore, MD, USA"},{"name":"Department of Computer Science and Mathematics , Freie Universit\u00e4t Berlin"},{"name":"Department of Computational Molecular Biology , Max Planck Institute for Molecular Genetics, Berlin, Germany"}]},{"given":"Mai","family":"Alzamel","sequence":"additional","affiliation":[{"name":"Department of Informatics , King\u2019s College London, London, UK"},{"name":"Department of Computer Science , King Saud University, Riyadh, Saudi Arabia"}]},{"given":"Costas S","family":"Iliopoulos","sequence":"additional","affiliation":[{"name":"Department of Informatics , King\u2019s College London, London, UK"}]},{"given":"Knut","family":"Reinert","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Mathematics , Freie Universit\u00e4t Berlin"},{"name":"Department of Computational Molecular Biology , Max Planck Institute for Molecular Genetics, Berlin, Germany"}]}],"member":"286","published-online":{"date-parts":[[2020,4,4]]},"reference":[{"key":"2023063010285213400_btaa222-B1","first-page":"1","volume-title":"Information Technology and Applications in Biomedicine (ITAB 2009)","author":"Antoniou","year":"2009"},{"key":"2023063010285213400_btaa222-B2","doi-asserted-by":"crossref","first-page":"4555","DOI":"10.1128\/AEM.66.10.4555-4558.2000","article-title":"Rapid and simple determination of the Escherichia coli phylogenetic group","volume":"66","author":"Clermont","year":"2000","journal-title":"Appl. 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