MersV1, Main, Exploration, bibRecord, 000F38

ntHash: recursive nucleotide hashing

Identifieur interne : 000F38 ( Main/Exploration ); précédent : 000F37; suivant : 000F39

ntHash: recursive nucleotide hashing

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

Source :

Bioinformatics [ 1367-4803 ] ; 2016.

RBID : PMC:5181554

Descripteurs français

KwdFr :
- Algorithmes, Alignement de séquences, Analyse de séquence d'ADN, Animaux, Humains, Logiciel, Nucléotides.
MESH :
- Algorithmes, Alignement de séquences, Analyse de séquence d'ADN, Animaux, Humains, Logiciel, Nucléotides.

English descriptors

KwdEn :
- Algorithms, Animals, Humans, Nucleotides, Sequence Alignment, Sequence Analysis, DNA, Software.
MESH :
- chemical : Nucleotides.
- Algorithms, Animals, Humans, Sequence Alignment, Sequence Analysis, DNA, Software.

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:

Le document en format XML

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<term>Alignement de séquences</term>
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<term>Alignement de séquences</term>
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<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>
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Serveur d'exploration MERS

ntHash: recursive nucleotide hashing

ntHash: recursive nucleotide hashing

Source :

Descripteurs français

English descriptors

Abstract

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

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

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Pour générer des pages wiki

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