MersV1, France, Analysis, bibRecord, 000041

AllSome Sequence Bloom Trees.

Identifieur interne : 000041 ( France/Analysis ); précédent : 000040; suivant : 000042

AllSome Sequence Bloom Trees.

Auteurs : Chen Sun [États-Unis] ; Robert S. Harris [États-Unis] ; Rayan Chikhi [France] ; Paul Medvedev [États-Unis]

Source :

Journal of computational biology : a journal of computational molecular cell biology [ 1557-8666 ] ; 2018.

RBID : pubmed:29620920

Descripteurs français

KwdFr :
- Algorithmes, Analyse de séquence d'ADN (), Bases de données d'acides nucléiques, Biologie informatique (), Encéphale (métabolisme), Femelle, Humains, Logiciel, Région mammaire (métabolisme), Sang (métabolisme), Séquençage nucléotidique à haut débit (), Transcriptome.
MESH :
- métabolisme : Encéphale, Région mammaire, Sang.
- Algorithmes, Analyse de séquence d'ADN, Bases de données d'acides nucléiques, Biologie informatique, Femelle, Humains, Logiciel, Séquençage nucléotidique à haut débit, Transcriptome.

English descriptors

KwdEn :
- Algorithms, Blood (metabolism), Brain (metabolism), Breast (metabolism), Computational Biology (methods), Databases, Nucleic Acid, Female, High-Throughput Nucleotide Sequencing (methods), Humans, Sequence Analysis, DNA (methods), Software, Transcriptome.
MESH :
- metabolism : Blood, Brain, Breast.
- methods : Computational Biology, High-Throughput Nucleotide Sequencing, Sequence Analysis, DNA.
- Algorithms, Databases, Nucleic Acid, Female, Humans, Software, Transcriptome.

Abstract

The ubiquity of next-generation sequencing has transformed the size and nature of many databases, pushing the boundaries of current indexing and searching methods. One particular example is a database of 2652 human RNA-seq experiments uploaded to the Sequence Read Archive (SRA). Recently, Solomon and Kingsford proposed the Sequence Bloom Tree data structure and demonstrated how it can be used to accurately identify SRA samples that have a transcript of interest potentially expressed. In this article, we propose an improvement called the AllSome Sequence Bloom Tree. Results show that our new data structure significantly improves performance, reducing the tree construction time by 52.7% and query time by 39%-85%, with a price of upto 3 × memory consumption during queries. Notably, it can query a batch of 198,074 queries in <8 hours (compared with around 2 days previously) and a whole set of k-mers from a sequencing experiment (about 27 million k-mers) in <11 minutes.

DOI: 10.1089/cmb.2017.0258
PubMed: 29620920

Affiliations:

Links to Exploration step

pubmed:29620920

Le document en format XML

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<term>Databases, Nucleic Acid</term>
<term>Female</term>
<term>High-Throughput Nucleotide Sequencing (methods)</term>
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<term>High-Throughput Nucleotide Sequencing</term>
<term>Sequence Analysis, DNA</term>
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<term>Région mammaire</term>
<term>Sang</term>
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<term>Analyse de séquence d'ADN</term>
<term>Bases de données d'acides nucléiques</term>
<term>Biologie informatique</term>
<term>Femelle</term>
<term>Humains</term>
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<term>Séquençage nucléotidique à haut débit</term>
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<front><div type="abstract" xml:lang="en">The ubiquity of next-generation sequencing has transformed the size and nature of many databases, pushing the boundaries of current indexing and searching methods. One particular example is a database of 2652 human RNA-seq experiments uploaded to the Sequence Read Archive (SRA). Recently, Solomon and Kingsford proposed the Sequence Bloom Tree data structure and demonstrated how it can be used to accurately identify SRA samples that have a transcript of interest potentially expressed. In this article, we propose an improvement called the AllSome Sequence Bloom Tree. Results show that our new data structure significantly improves performance, reducing the tree construction time by 52.7% and query time by 39%-85%, with a price of upto 3 × memory consumption during queries. Notably, it can query a batch of 198,074 queries in <8 hours (compared with around 2 days previously) and a whole set of k-mers from a sequencing experiment (about 27 million k-mers) in <11 minutes.</div>
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Serveur d'exploration MERS

AllSome Sequence Bloom Trees.

AllSome Sequence Bloom Trees.

Source :

Descripteurs français

English descriptors

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

	Serveur d'exploration MERS
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