Best hits of 11110110111: model-free selection and parameter-free sensitivity calculation of spaced seeds.
Identifieur interne : 000D81 ( PubMed/Checkpoint ); précédent : 000D80; suivant : 000D82Best hits of 11110110111: model-free selection and parameter-free sensitivity calculation of spaced seeds.
Auteurs : Laurent Noé [France]Source :
- Algorithms for molecular biology : AMB [ 1748-7188 ] ; 2017.
Abstract
Spaced seeds, also named gapped q-grams, gapped k-mers, spaced q-grams, have been proven to be more sensitive than contiguous seeds (contiguous q-grams, contiguous k-mers) in nucleic and amino-acid sequences analysis. Initially proposed to detect sequence similarities and to anchor sequence alignments, spaced seeds have more recently been applied in several alignment-free related methods. Unfortunately, spaced seeds need to be initially designed. This task is known to be time-consuming due to the number of spaced seed candidates. Moreover, it can be altered by a set of arbitrary chosen parameters from the probabilistic alignment models used. In this general context, Dominant seeds have been introduced by Mak and Benson (Bioinformatics 25:302-308, 2009) on the Bernoulli model, in order to reduce the number of spaced seed candidates that are further processed in a parameter-free calculation of the sensitivity.
DOI: 10.1186/s13015-017-0092-1
PubMed: 28289437
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Best hits of 11110110111: model-free selection and parameter-free sensitivity calculation of spaced seeds.</title><author><name sortKey="Noe, Laurent" sort="Noe, Laurent" uniqKey="Noe L" first="Laurent" last="Noé">Laurent Noé</name><affiliation wicri:level="3"><nlm:affiliation>CRIStAL (UMR 9189 Lille University/CNRS)-Inria Lille, Bat M3 ext, Université Lille 1, 59655 Villeneuve d'Ascq, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>CRIStAL (UMR 9189 Lille University/CNRS)-Inria Lille, Bat M3 ext, Université Lille 1, 59655 Villeneuve d'Ascq</wicri:regionArea><placeName><region type="region" nuts="2">Hauts-de-France</region><region type="old region" nuts="2">Nord-Pas-de-Calais</region><settlement type="city">Villeneuve d'Ascq</settlement></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2017">2017</date><idno type="RBID">pubmed:28289437</idno><idno type="pmid">28289437</idno><idno type="doi">10.1186/s13015-017-0092-1</idno><idno type="wicri:Area/PubMed/Corpus">000D54</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000D54</idno><idno type="wicri:Area/PubMed/Curation">000D54</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000D54</idno><idno type="wicri:Area/PubMed/Checkpoint">000D81</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">000D81</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Best hits of 11110110111: model-free selection and parameter-free sensitivity calculation of spaced seeds.</title><author><name sortKey="Noe, Laurent" sort="Noe, Laurent" uniqKey="Noe L" first="Laurent" last="Noé">Laurent Noé</name><affiliation wicri:level="3"><nlm:affiliation>CRIStAL (UMR 9189 Lille University/CNRS)-Inria Lille, Bat M3 ext, Université Lille 1, 59655 Villeneuve d'Ascq, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>CRIStAL (UMR 9189 Lille University/CNRS)-Inria Lille, Bat M3 ext, Université Lille 1, 59655 Villeneuve d'Ascq</wicri:regionArea><placeName><region type="region" nuts="2">Hauts-de-France</region><region type="old region" nuts="2">Nord-Pas-de-Calais</region><settlement type="city">Villeneuve d'Ascq</settlement></placeName></affiliation></author></analytic><series><title level="j">Algorithms for molecular biology : AMB</title><idno type="ISSN">1748-7188</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><i>Spaced seeds</i>, also named <i>gapped q-grams, gapped k-mers, spaced q-grams</i>, have been proven to be more sensitive than contiguous seeds (<i>contiguous q-grams, contiguous k-mers</i>) in nucleic and amino-acid sequences analysis. Initially proposed to detect sequence similarities and to anchor sequence alignments, spaced seeds have more recently been applied in several <i>alignment-free</i> related methods. Unfortunately, spaced seeds need to be initially designed. This task is known to be time-consuming due to the number of spaced seed candidates. Moreover, it can be altered by a set of <i>arbitrary chosen</i> parameters from the probabilistic alignment models used. In this general context, <i>Dominant seeds</i> have been introduced by Mak and Benson (Bioinformatics 25:302-308, 2009) on the Bernoulli model, in order to reduce the number of spaced seed candidates that are further processed in a <i>parameter-free</i> calculation of the sensitivity.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">28289437</PMID><DateRevised><Year>2019</Year><Month>11</Month><Day>20</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">1748-7188</ISSN><JournalIssue CitedMedium="Print"><Volume>12</Volume><PubDate><Year>2017</Year></PubDate></JournalIssue><Title>Algorithms for molecular biology : AMB</Title><ISOAbbreviation>Algorithms Mol Biol</ISOAbbreviation></Journal><ArticleTitle>Best hits of 11110110111: model-free selection and parameter-free sensitivity calculation of spaced seeds.</ArticleTitle><Pagination><MedlinePgn>1</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/s13015-017-0092-1</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND"><i>Spaced seeds</i>, also named <i>gapped q-grams, gapped k-mers, spaced q-grams</i>, have been proven to be more sensitive than contiguous seeds (<i>contiguous q-grams, contiguous k-mers</i>) in nucleic and amino-acid sequences analysis. Initially proposed to detect sequence similarities and to anchor sequence alignments, spaced seeds have more recently been applied in several <i>alignment-free</i> related methods. Unfortunately, spaced seeds need to be initially designed. This task is known to be time-consuming due to the number of spaced seed candidates. Moreover, it can be altered by a set of <i>arbitrary chosen</i> parameters from the probabilistic alignment models used. In this general context, <i>Dominant seeds</i> have been introduced by Mak and Benson (Bioinformatics 25:302-308, 2009) on the Bernoulli model, in order to reduce the number of spaced seed candidates that are further processed in a <i>parameter-free</i> calculation of the sensitivity.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">We expand the scope of work of Mak and Benson on single and multiple seeds by considering the Hit Integration model of Chung and Park (BMC Bioinform 11:31, 2010), demonstrate that the same dominance definition can be applied, and that a parameter-free study can be performed without any significant additional cost. We also consider two new discrete models, namely the Heaviside and the Dirac models, where lossless seeds can be integrated. From a theoretical standpoint, we establish a generic framework on all the proposed models, by applying a <i>counting semi-ring</i> to quickly compute large polynomial coefficients needed by the <i>dominance</i> filter. From a practical standpoint, we confirm that <i>dominant seeds</i> reduce the set of, either single seeds to thoroughly analyse, or multiple seeds to store. Moreover, in http://bioinfo.cristal.univ-lille.fr/yass/iedera_dominance, we provide a full list of spaced seeds computed on the four aforementioned models, with one (continuous) parameter left free for each model, and with several (discrete) alignment lengths.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Noé</LastName><ForeName>Laurent</ForeName><Initials>L</Initials><Identifier Source="ORCID">0000-0002-1170-8376</Identifier><AffiliationInfo><Affiliation>CRIStAL (UMR 9189 Lille University/CNRS)-Inria Lille, Bat M3 ext, Université Lille 1, 59655 Villeneuve d'Ascq, France.</Affiliation><Identifier Source="ISNI">0000 0001 2186 1211</Identifier><Identifier Source="GRID">grid.4461.7</Identifier></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>02</Month><Day>14</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Algorithms Mol Biol</MedlineTA><NlmUniqueID>101265088</NlmUniqueID><ISSNLinking>1748-7188</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Bernoulli</Keyword><Keyword MajorTopicYN="N">Counting semi-ring</Keyword><Keyword MajorTopicYN="N">DFA</Keyword><Keyword MajorTopicYN="N">Dirac</Keyword><Keyword MajorTopicYN="N">Dominant seeds</Keyword><Keyword MajorTopicYN="N">Heaviside</Keyword><Keyword MajorTopicYN="N">Hit Integration</Keyword><Keyword MajorTopicYN="N">Polynomial form</Keyword><Keyword MajorTopicYN="N">Spaced seeds</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2016</Year><Month>09</Month><Day>19</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2017</Year><Month>01</Month><Day>30</Day></PubMedPubDate><PubMedPubDate 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