GenMap: Ultra-fast Computation of Genome Mappability.
Identifieur interne : 000091 ( PubMed/Curation ); précédent : 000090; suivant : 000092GenMap: 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
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Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD</wicri:regionArea></affiliation></author><author><name sortKey="Alzamel, Mai" sort="Alzamel, Mai" uniqKey="Alzamel M" first="Mai" last="Alzamel">Mai Alzamel</name><affiliation wicri:level="1"><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></affiliation></author><author><name sortKey="Iliopoulos, Costas S" sort="Iliopoulos, Costas S" uniqKey="Iliopoulos C" first="Costas S" last="Iliopoulos">Costas S. 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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></affiliation></author><author><name sortKey="Alzamel, Mai" sort="Alzamel, Mai" uniqKey="Alzamel M" first="Mai" last="Alzamel">Mai Alzamel</name><affiliation wicri:level="1"><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></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="1"><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></affiliation></author><author><name sortKey="Reinert, Knut" sort="Reinert, Knut" uniqKey="Reinert K" first="Knut" last="Reinert">Knut Reinert</name><affiliation wicri:level="1"><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></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><pubmed><MedlineCitation Status="Publisher" Owner="NLM"><PMID Version="1">32246826</PMID><DateRevised><Year>2020</Year><Month>04</Month><Day>04</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1367-4811</ISSN><JournalIssue CitedMedium="Internet"><PubDate><Year>2020</Year><Month>Apr</Month><Day>04</Day></PubDate></JournalIssue><Title>Bioinformatics (Oxford, England)</Title><ISOAbbreviation>Bioinformatics</ISOAbbreviation></Journal><ArticleTitle>GenMap: Ultra-fast Computation of Genome Mappability.</ArticleTitle><ELocationID EIdType="pii" ValidYN="Y">btaa222</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.1093/bioinformatics/btaa222</ELocationID><Abstract><AbstractText Label="MOTIVATION" NlmCategory="BACKGROUND">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.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">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.</AbstractText><AbstractText Label="AVAILABILITY" NlmCategory="BACKGROUND">GenMap can be installed via bioconda. Binaries and C ++ source code are available on https://github.com/cpockrandt/genmap.</AbstractText><CopyrightInformation>© The Author(s) 2020. Published by Oxford University Press.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Pockrandt</LastName><ForeName>Christopher</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Center for Computational Biology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA. Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Computer Science and Mathematics, Freie Universität Berlin, Berlin, Germany.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Max Planck Institute for Molecular Genetics, Berlin, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Alzamel</LastName><ForeName>Mai</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Informatics, King's College London, London, UK.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Computer Science, King Saud University, Riyadh, SA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Iliopoulos</LastName><ForeName>Costas S</ForeName><Initials>CS</Initials><AffiliationInfo><Affiliation>Department of Informatics, King's College London, London, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Reinert</LastName><ForeName>Knut</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Department of Computer Science and Mathematics, Freie Universität Berlin, Berlin, Germany.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Max Planck Institute for Molecular Genetics, Berlin, Germany.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>04</Month><Day>04</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Bioinformatics</MedlineTA><NlmUniqueID>9808944</NlmUniqueID><ISSNLinking>1367-4803</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2019</Year><Month>12</Month><Day>14</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2020</Year><Month>03</Month><Day>23</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>03</Month><Day>25</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>4</Month><Day>5</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>4</Month><Day>5</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>4</Month><Day>5</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>aheadofprint</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32246826</ArticleId><ArticleId IdType="pii">5815974</ArticleId><ArticleId IdType="doi">10.1093/bioinformatics/btaa222</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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