GenMap: Ultra-fast Computation of Genome Mappability.
Identifieur interne : 000195 ( Main/Exploration ); précédent : 000194; suivant : 000196GenMap: Ultra-fast Computation of Genome Mappability.
Auteurs : Christopher Pockrandt [États-Unis] ; Mai Alzamel [Royaume-Uni] ; Costas S. Iliopoulos [Royaume-Uni] ; Knut Reinert [Allemagne]Source :
- Bioinformatics (Oxford, England) [ 1367-4811 ] ; 2020.
Abstract
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.
DOI: 10.1093/bioinformatics/btaa222
PubMed: 32246826
Affiliations:
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Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Computational Biology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA. Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD</wicri:regionArea><placeName><region type="state">Maryland</region></placeName></affiliation></author><author><name sortKey="Alzamel, Mai" sort="Alzamel, Mai" uniqKey="Alzamel M" first="Mai" last="Alzamel">Mai Alzamel</name><affiliation wicri:level="3"><nlm:affiliation>Department of Informatics, King's College London, London, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Department of Informatics, King's College London, London</wicri:regionArea><placeName><settlement type="city">Londres</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Londres</region></placeName></affiliation></author><author><name sortKey="Iliopoulos, Costas S" sort="Iliopoulos, Costas S" uniqKey="Iliopoulos C" first="Costas S" last="Iliopoulos">Costas S. Iliopoulos</name><affiliation wicri:level="3"><nlm:affiliation>Department of Informatics, King's College London, London, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Department of Informatics, King's College London, London</wicri:regionArea><placeName><settlement type="city">Londres</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Londres</region></placeName></affiliation></author><author><name sortKey="Reinert, Knut" sort="Reinert, Knut" uniqKey="Reinert K" first="Knut" last="Reinert">Knut Reinert</name><affiliation wicri:level="3"><nlm:affiliation>Department of Computer Science and Mathematics, Freie Universität Berlin, Berlin, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Department of Computer Science and Mathematics, Freie Universität Berlin, Berlin</wicri:regionArea><placeName><region type="land" nuts="3">Berlin</region><settlement type="city">Berlin</settlement></placeName></affiliation></author></analytic><series><title level="j">Bioinformatics (Oxford, England)</title><idno type="eISSN">1367-4811</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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.</div></front></TEI><affiliations><list><country><li>Allemagne</li><li>Royaume-Uni</li><li>États-Unis</li></country><region><li>Angleterre</li><li>Berlin</li><li>Grand Londres</li><li>Maryland</li></region><settlement><li>Berlin</li><li>Londres</li></settlement></list><tree><country name="États-Unis"><region name="Maryland"><name sortKey="Pockrandt, Christopher" sort="Pockrandt, Christopher" uniqKey="Pockrandt C" first="Christopher" last="Pockrandt">Christopher Pockrandt</name></region></country><country name="Royaume-Uni"><region name="Angleterre"><name sortKey="Alzamel, Mai" sort="Alzamel, Mai" uniqKey="Alzamel M" first="Mai" last="Alzamel">Mai Alzamel</name></region><name sortKey="Iliopoulos, Costas S" sort="Iliopoulos, Costas S" uniqKey="Iliopoulos C" first="Costas S" last="Iliopoulos">Costas S. Iliopoulos</name></country><country name="Allemagne"><region name="Berlin"><name sortKey="Reinert, Knut" sort="Reinert, Knut" uniqKey="Reinert K" first="Knut" last="Reinert">Knut Reinert</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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