TelematiV1, PubMed, Corpus, bibRecord, 000245

A genomic distance for assembly comparison based on compressed maximal exact matches.

Identifieur interne : 000245 ( PubMed/Corpus ); précédent : 000244; suivant : 000246

A genomic distance for assembly comparison based on compressed maximal exact matches.

Auteurs : S P Garcia ; J M O S. Rodrigues ; S. Santos ; D. Pratas ; V. Afreixo ; C A C. Bastos ; P J S G. Ferreira ; A J Pinho

Source :

IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM [ 1557-9964 ]

RBID : pubmed:25594089

English descriptors

KwdEn :
- Algorithms, Genome, Human (genetics), Genomics (methods), Humans, Sequence Analysis, DNA (methods).
MESH :
- genetics : Genome, Human.
- methods : Genomics, Sequence Analysis, DNA.
- Algorithms, Humans.

Abstract

Genome assemblies are typically compared with respect to their contiguity, coverage, and accuracy. We propose a genome-wide, alignment-free genomic distance based on compressed maximal exact matches and suggest adding it to the benchmark of commonly used assembly quality metrics. Maximal exact matches are perfect repeats, without gaps or misspellings, which cannot be further extended to either their left- or right-end side without loss of similarity. The genomic distance here proposed is based on the normalized compression distance, an information-theoretic measure of the relative compressibility of two sequences estimated using multiple finite-context models. This measure exposes similarities between the sequences, as well as, the nesting structure underlying the assembly of larger maximal exact matches from smaller ones. We use four human genome assemblies for illustration and discuss the impact of genome sequencing and assembly in the final content of maximal exact matches and the genomic distance here proposed.

PubMed: 25594089

Links to Exploration step

pubmed:25594089

Le document en format XML

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<author><name sortKey="Garcia, S P" sort="Garcia, S P" uniqKey="Garcia S" first="S P" last="Garcia">S P Garcia</name>
<affiliation><nlm:affiliation>Signal Processing Laboratory, Institute of Electronics and Telematics Engineering of Aveiro, University of Aveiro, 3810-193 Aveiro, Portugal. spgarcia@ua.pt</nlm:affiliation>
</affiliation>
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<author><name sortKey="Rodrigues, J M O S" sort="Rodrigues, J M O S" uniqKey="Rodrigues J" first="J M O S" last="Rodrigues">J M O S. Rodrigues</name>
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<author><name sortKey="Santos, S" sort="Santos, S" uniqKey="Santos S" first="S" last="Santos">S. Santos</name>
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<author><name sortKey="Pratas, D" sort="Pratas, D" uniqKey="Pratas D" first="D" last="Pratas">D. Pratas</name>
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<author><name sortKey="Afreixo, V" sort="Afreixo, V" uniqKey="Afreixo V" first="V" last="Afreixo">V. Afreixo</name>
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<author><name sortKey="Bastos, C A C" sort="Bastos, C A C" uniqKey="Bastos C" first="C A C" last="Bastos">C A C. Bastos</name>
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<author><name sortKey="Ferreira, P J S G" sort="Ferreira, P J S G" uniqKey="Ferreira P" first="P J S G" last="Ferreira">P J S G. Ferreira</name>
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<author><name sortKey="Pinho, A J" sort="Pinho, A J" uniqKey="Pinho A" first="A J" last="Pinho">A J Pinho</name>
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<author><name sortKey="Rodrigues, J M O S" sort="Rodrigues, J M O S" uniqKey="Rodrigues J" first="J M O S" last="Rodrigues">J M O S. Rodrigues</name>
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<author><name sortKey="Santos, S" sort="Santos, S" uniqKey="Santos S" first="S" last="Santos">S. Santos</name>
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<author><name sortKey="Afreixo, V" sort="Afreixo, V" uniqKey="Afreixo V" first="V" last="Afreixo">V. Afreixo</name>
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<term>Sequence Analysis, DNA (methods)</term>
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<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Genome, Human</term>
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<keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Genomics</term>
<term>Sequence Analysis, DNA</term>
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<front><div type="abstract" xml:lang="en">Genome assemblies are typically compared with respect to their contiguity, coverage, and accuracy. We propose a genome-wide, alignment-free genomic distance based on compressed maximal exact matches and suggest adding it to the benchmark of commonly used assembly quality metrics. Maximal exact matches are perfect repeats, without gaps or misspellings, which cannot be further extended to either their left- or right-end side without loss of similarity. The genomic distance here proposed is based on the normalized compression distance, an information-theoretic measure of the relative compressibility of two sequences estimated using multiple finite-context models. This measure exposes similarities between the sequences, as well as, the nesting structure underlying the assembly of larger maximal exact matches from smaller ones. We use four human genome assemblies for illustration and discuss the impact of genome sequencing and assembly in the final content of maximal exact matches and the genomic distance here proposed.</div>
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<Month>07</Month>
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<Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1557-9964</ISSN>
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<Title>IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM</Title>
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<ArticleTitle>A genomic distance for assembly comparison based on compressed maximal exact matches.</ArticleTitle>
<Pagination><MedlinePgn>793-8</MedlinePgn>
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<Abstract><AbstractText>Genome assemblies are typically compared with respect to their contiguity, coverage, and accuracy. We propose a genome-wide, alignment-free genomic distance based on compressed maximal exact matches and suggest adding it to the benchmark of commonly used assembly quality metrics. Maximal exact matches are perfect repeats, without gaps or misspellings, which cannot be further extended to either their left- or right-end side without loss of similarity. The genomic distance here proposed is based on the normalized compression distance, an information-theoretic measure of the relative compressibility of two sequences estimated using multiple finite-context models. This measure exposes similarities between the sequences, as well as, the nesting structure underlying the assembly of larger maximal exact matches from smaller ones. We use four human genome assemblies for illustration and discuss the impact of genome sequencing and assembly in the final content of maximal exact matches and the genomic distance here proposed.</AbstractText>
</Abstract>
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A genomic distance for assembly comparison based on compressed maximal exact matches.

A genomic distance for assembly comparison based on compressed maximal exact matches.

Source :

English descriptors

Abstract

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