MersV1, Pmc, Checkpoint, bibRecord, 000955

ntHash: recursive nucleotide hashing

Identifieur interne : 000955 ( Pmc/Checkpoint ); précédent : 000954; suivant : 000956

ntHash: recursive nucleotide hashing

Auteurs : Hamid Mohamadi ; Justin Chu ; Benjamin P. Vandervalk ; Inanc Birol

Source :

Bioinformatics [ 1367-4803 ] ; 2016.

RBID : PMC:5181554

Abstract

Motivation: Hashing has been widely used for indexing, querying and rapid similarity search in many bioinformatics applications, including sequence alignment, genome and transcriptome assembly, k-mer counting and error correction. Hence, expediting hashing operations would have a substantial impact in the field, making bioinformatics applications faster and more efficient.

Results: We present ntHash, a hashing algorithm tuned for processing DNA/RNA sequences. It performs the best when calculating hash values for adjacent k-mers in an input sequence, operating an order of magnitude faster than the best performing alternatives in typical use cases.

Availability and implementation: ntHash is available online at http://www.bcgsc.ca/platform/bioinfo/software/nthash and is free for academic use.

Contacts: hmohamadi@bcgsc.ca or ibirol@bcgsc.ca

Supplementary information:Supplementary data are available at Bioinformatics online.

Url:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5181554

DOI: 10.1093/bioinformatics/btw397
PubMed: 27423894
PubMed Central: 5181554

Affiliations:

Links toward previous steps (curation, corpus...)

to stream Pmc, to step Corpus: 000B14
to stream Pmc, to step Curation: 000B14

Links to Exploration step

PMC:5181554

Le document en format XML

<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">ntHash: recursive nucleotide hashing</title>
<author><name sortKey="Mohamadi, Hamid" sort="Mohamadi, Hamid" uniqKey="Mohamadi H" first="Hamid" last="Mohamadi">Hamid Mohamadi</name>
</author>
<author><name sortKey="Chu, Justin" sort="Chu, Justin" uniqKey="Chu J" first="Justin" last="Chu">Justin Chu</name>
</author>
<author><name sortKey="Vandervalk, Benjamin P" sort="Vandervalk, Benjamin P" uniqKey="Vandervalk B" first="Benjamin P." last="Vandervalk">Benjamin P. Vandervalk</name>
</author>
<author><name sortKey="Birol, Inanc" sort="Birol, Inanc" uniqKey="Birol I" first="Inanc" last="Birol">Inanc Birol</name>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PMC</idno>
<idno type="pmid">27423894</idno>
<idno type="pmc">5181554</idno>
<idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5181554</idno>
<idno type="RBID">PMC:5181554</idno>
<idno type="doi">10.1093/bioinformatics/btw397</idno>
<date when="2016">2016</date>
<idno type="wicri:Area/Pmc/Corpus">000B14</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000B14</idno>
<idno type="wicri:Area/Pmc/Curation">000B14</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000B14</idno>
<idno type="wicri:Area/Pmc/Checkpoint">000955</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000955</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">ntHash: recursive nucleotide hashing</title>
<author><name sortKey="Mohamadi, Hamid" sort="Mohamadi, Hamid" uniqKey="Mohamadi H" first="Hamid" last="Mohamadi">Hamid Mohamadi</name>
</author>
<author><name sortKey="Chu, Justin" sort="Chu, Justin" uniqKey="Chu J" first="Justin" last="Chu">Justin Chu</name>
</author>
<author><name sortKey="Vandervalk, Benjamin P" sort="Vandervalk, Benjamin P" uniqKey="Vandervalk B" first="Benjamin P." last="Vandervalk">Benjamin P. Vandervalk</name>
</author>
<author><name sortKey="Birol, Inanc" sort="Birol, Inanc" uniqKey="Birol I" first="Inanc" last="Birol">Inanc Birol</name>
</author>
</analytic>
<series><title level="j">Bioinformatics</title>
<idno type="ISSN">1367-4803</idno>
<idno type="eISSN">1367-4811</idno>
<imprint><date when="2016">2016</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><p><bold>Motivation</bold>
: Hashing has been widely used for indexing, querying and rapid similarity search in many bioinformatics applications, including sequence alignment, genome and transcriptome assembly, <italic>k</italic>
-mer counting and error correction. Hence, expediting hashing operations would have a substantial impact in the field, making bioinformatics applications faster and more efficient.</p>
<p><bold>Results</bold>
: We present ntHash, a hashing algorithm tuned for processing DNA/RNA sequences. It performs the best when calculating hash values for adjacent <italic>k</italic>
-mers in an input sequence, operating an order of magnitude faster than the best performing alternatives in typical use cases.</p>
<p><bold>Availability and implementation</bold>
: ntHash is available online at <ext-link ext-link-type="uri" xlink:href="http://www.bcgsc.ca/platform/bioinfo/software/nthash">http://www.bcgsc.ca/platform/bioinfo/software/nthash</ext-link>
 and is free for academic use.</p>
<p><bold>Contacts</bold>
: <email>hmohamadi@bcgsc.ca</email>
 or <email>ibirol@bcgsc.ca</email>
</p>
<p><bold>Supplementary information:</bold>
<ext-link ext-link-type="uri" xlink:href="http://bioinformatics.oxfordjournals.org/lookup/suppl/doi:10.1093/bioinformatics/btw397/-/DC1">Supplementary data</ext-link>
 are available at <italic>Bioinformatics</italic>
 online.</p>
</div>
</front>
<back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Cohen, J D" uniqKey="Cohen J">J.D. Cohen</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Gonnet, G H" uniqKey="Gonnet G">G.H. Gonnet</name>
</author>
<author><name sortKey="Baezayates, R A" uniqKey="Baezayates R">R.A. Baezayates</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Karp, R M" uniqKey="Karp R">R.M. Karp</name>
</author>
<author><name sortKey="Rabin, M O" uniqKey="Rabin M">M.O. Rabin</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Lemire, D" uniqKey="Lemire D">D. Lemire</name>
</author>
<author><name sortKey="Kaser, O" uniqKey="Kaser O">O. Kaser</name>
</author>
</analytic>
</biblStruct>
</listBibl>
</div1>
</back>
</TEI>
<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
  <front><journal-meta><journal-id journal-id-type="nlm-ta">Bioinformatics</journal-id>
<journal-id journal-id-type="iso-abbrev">Bioinformatics</journal-id>
<journal-id journal-id-type="publisher-id">bioinformatics</journal-id>
<journal-id journal-id-type="hwp">bioinfo</journal-id>
<journal-title-group><journal-title>Bioinformatics</journal-title>
</journal-title-group>
<issn pub-type="ppub">1367-4803</issn>
<issn pub-type="epub">1367-4811</issn>
<publisher><publisher-name>Oxford University Press</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">27423894</article-id>
<article-id pub-id-type="pmc">5181554</article-id>
<article-id pub-id-type="doi">10.1093/bioinformatics/btw397</article-id>
<article-id pub-id-type="publisher-id">btw397</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Applications Notes</subject>
<subj-group subj-group-type="heading"><subject>Sequence Analysis</subject>
</subj-group>
</subj-group>
</article-categories>
<title-group><article-title>ntHash: recursive nucleotide hashing</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Mohamadi</surname>
<given-names>Hamid</given-names>
</name>
<xref ref-type="corresp" rid="btw397-cor1">*</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Chu</surname>
<given-names>Justin</given-names>
</name>
</contrib>
<contrib contrib-type="author"><name><surname>Vandervalk</surname>
<given-names>Benjamin P.</given-names>
</name>
</contrib>
<contrib contrib-type="author"><name><surname>Birol</surname>
<given-names>Inanc</given-names>
</name>
<xref ref-type="corresp" rid="btw397-cor1">*</xref>
</contrib>
<aff id="btw397-aff1">Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4S6, Canada</aff>
</contrib-group>
<author-notes><corresp id="btw397-cor1">*To whom correspondence should be addressed.</corresp>
<fn id="btw397-FM1"><p>Associate Editor: Bonnie Berger</p>
</fn>
</author-notes>
<pub-date pub-type="ppub"><day>15</day>
<month>11</month>
<year>2016</year>
</pub-date>
<pub-date pub-type="epub"><day>16</day>
<month>7</month>
<year>2016</year>
</pub-date>
<pub-date pub-type="pmc-release"><day>16</day>
<month>7</month>
<year>2016</year>
</pub-date>
<pmc-comment> PMC Release delay is 0 months and 0 days and was based on the . </pmc-comment>
      <volume>32</volume>
<issue>22</issue>
<fpage>3492</fpage>
<lpage>3494</lpage>
<history><date date-type="received"><day>3</day>
<month>2</month>
<year>2016</year>
</date>
<date date-type="rev-recd"><day>14</day>
<month>6</month>
<year>2016</year>
</date>
<date date-type="accepted"><day>17</day>
<month>6</month>
<year>2016</year>
</date>
</history>
<permissions><copyright-statement>© The Author 2016. Published by Oxford University Press.</copyright-statement>
<copyright-year>2016</copyright-year>
<license xlink:href="http://creativecommons.org/licenses/by-nc/4.0/" license-type="creative-commons"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by-nc/4.0/">http://creativecommons.org/licenses/by-nc/4.0/</ext-link>
), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com</license-p>
</license>
</permissions>
<abstract><p><bold>Motivation</bold>
: Hashing has been widely used for indexing, querying and rapid similarity search in many bioinformatics applications, including sequence alignment, genome and transcriptome assembly, <italic>k</italic>
-mer counting and error correction. Hence, expediting hashing operations would have a substantial impact in the field, making bioinformatics applications faster and more efficient.</p>
<p><bold>Results</bold>
: We present ntHash, a hashing algorithm tuned for processing DNA/RNA sequences. It performs the best when calculating hash values for adjacent <italic>k</italic>
-mers in an input sequence, operating an order of magnitude faster than the best performing alternatives in typical use cases.</p>
<p><bold>Availability and implementation</bold>
: ntHash is available online at <ext-link ext-link-type="uri" xlink:href="http://www.bcgsc.ca/platform/bioinfo/software/nthash">http://www.bcgsc.ca/platform/bioinfo/software/nthash</ext-link>
 and is free for academic use.</p>
<p><bold>Contacts</bold>
: <email>hmohamadi@bcgsc.ca</email>
 or <email>ibirol@bcgsc.ca</email>
</p>
<p><bold>Supplementary information:</bold>
<ext-link ext-link-type="uri" xlink:href="http://bioinformatics.oxfordjournals.org/lookup/suppl/doi:10.1093/bioinformatics/btw397/-/DC1">Supplementary data</ext-link>
 are available at <italic>Bioinformatics</italic>
 online.</p>
</abstract>
<counts><page-count count="3"></page-count>
</counts>
</article-meta>
</front>
</pmc>
<affiliations><list></list>
<tree><noCountry><name sortKey="Birol, Inanc" sort="Birol, Inanc" uniqKey="Birol I" first="Inanc" last="Birol">Inanc Birol</name>
<name sortKey="Chu, Justin" sort="Chu, Justin" uniqKey="Chu J" first="Justin" last="Chu">Justin Chu</name>
<name sortKey="Mohamadi, Hamid" sort="Mohamadi, Hamid" uniqKey="Mohamadi H" first="Hamid" last="Mohamadi">Hamid Mohamadi</name>
<name sortKey="Vandervalk, Benjamin P" sort="Vandervalk, Benjamin P" uniqKey="Vandervalk B" first="Benjamin P." last="Vandervalk">Benjamin P. Vandervalk</name>
</noCountry>
</tree>
</affiliations>
</record>

Pour manipuler ce document sous Unix (Dilib)

EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Pmc/Checkpoint

HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000955 | SxmlIndent | more

HfdSelect -h $EXPLOR_AREA/Data/Pmc/Checkpoint/biblio.hfd -nk 000955 | SxmlIndent | more

Pour mettre un lien sur cette page dans le réseau Wicri

{{Explor lien
   |wiki=    Sante
   |area=    MersV1
   |flux=    Pmc
   |étape=   Checkpoint
   |type=    RBID
   |clé=     PMC:5181554
   |texte=   ntHash: recursive nucleotide hashing
}}

Pour générer des pages wiki

HfdIndexSelect -h $EXPLOR_AREA/Data/Pmc/Checkpoint/RBID.i   -Sk "pubmed:27423894" \
       | HfdSelect -Kh $EXPLOR_AREA/Data/Pmc/Checkpoint/biblio.hfd   \
       | NlmPubMed2Wicri -a MersV1

This area was generated with Dilib version V0.6.33.
Data generation: Mon Apr 20 23:26:43 2020. Site generation: Sat Mar 27 09:06:09 2021

	Serveur d'exploration MERS
	Attention, ce site est en cours de développement ! Attention, site généré par des moyens informatiques à partir de corpus bruts. Les informations ne sont donc pas validées.

Serveur d'exploration MERS

ntHash: recursive nucleotide hashing

ntHash: recursive nucleotide hashing

Source :

Abstract

Links toward previous steps (curation, corpus...)

Links to Exploration step

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri

Pour générer des pages wiki