MersV1, PubMed, Corpus, bibRecord, 000495

Polymorphic edge detection (PED): two efficient methods of polymorphism detection from next-generation sequencing data.

Identifieur interne : 000495 ( PubMed/Corpus ); précédent : 000494; suivant : 000496

Polymorphic edge detection (PED): two efficient methods of polymorphism detection from next-generation sequencing data.

Auteurs : Akio Miyao ; Jianyu Song Kiyomiya ; Keiko Iida ; Koji Doi ; Hiroshi Yasue

Source :

BMC bioinformatics [ 1471-2105 ] ; 2019.

RBID : pubmed:31253084

English descriptors

KwdEn :
- Computational Biology (methods), High-Throughput Nucleotide Sequencing, Polymorphism, Single Nucleotide, Sequence Analysis, DNA, Software.
MESH :
- methods : Computational Biology.
- High-Throughput Nucleotide Sequencing, Polymorphism, Single Nucleotide, Sequence Analysis, DNA, Software.

Abstract

Accurate detection of polymorphisms with a next generation sequencer data is an important element of current genetic analysis. However, there is still no detection pipeline that is completely reliable.

DOI: 10.1186/s12859-019-2955-6
PubMed: 31253084

Links to Exploration step

pubmed:31253084

Le document en format XML

<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Polymorphic edge detection (PED): two efficient methods of polymorphism detection from next-generation sequencing data.</title>
<author><name sortKey="Miyao, Akio" sort="Miyao, Akio" uniqKey="Miyao A" first="Akio" last="Miyao">Akio Miyao</name>
<affiliation><nlm:affiliation>Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2, Kannondai, Tsukuba, Ibaraki, 305-8518, Japan. miyao@affrc.go.jp.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Kiyomiya, Jianyu Song" sort="Kiyomiya, Jianyu Song" uniqKey="Kiyomiya J" first="Jianyu Song" last="Kiyomiya">Jianyu Song Kiyomiya</name>
<affiliation><nlm:affiliation>Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2, Kannondai, Tsukuba, Ibaraki, 305-8518, Japan.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Iida, Keiko" sort="Iida, Keiko" uniqKey="Iida K" first="Keiko" last="Iida">Keiko Iida</name>
<affiliation><nlm:affiliation>Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2, Kannondai, Tsukuba, Ibaraki, 305-8518, Japan.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Doi, Koji" sort="Doi, Koji" uniqKey="Doi K" first="Koji" last="Doi">Koji Doi</name>
<affiliation><nlm:affiliation>Tsukuba Gene Technology Laboratories Inc, 6-320, Arakawaoki, Tsuchiura, Ibaraki, 300-0873, Japan.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Yasue, Hiroshi" sort="Yasue, Hiroshi" uniqKey="Yasue H" first="Hiroshi" last="Yasue">Hiroshi Yasue</name>
<affiliation><nlm:affiliation>Tsukuba Gene Technology Laboratories Inc, 6-320, Arakawaoki, Tsuchiura, Ibaraki, 300-0873, Japan.</nlm:affiliation>
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<sourceDesc><biblStruct><analytic><title xml:lang="en">Polymorphic edge detection (PED): two efficient methods of polymorphism detection from next-generation sequencing data.</title>
<author><name sortKey="Miyao, Akio" sort="Miyao, Akio" uniqKey="Miyao A" first="Akio" last="Miyao">Akio Miyao</name>
<affiliation><nlm:affiliation>Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2, Kannondai, Tsukuba, Ibaraki, 305-8518, Japan. miyao@affrc.go.jp.</nlm:affiliation>
</affiliation>
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<author><name sortKey="Kiyomiya, Jianyu Song" sort="Kiyomiya, Jianyu Song" uniqKey="Kiyomiya J" first="Jianyu Song" last="Kiyomiya">Jianyu Song Kiyomiya</name>
<affiliation><nlm:affiliation>Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2, Kannondai, Tsukuba, Ibaraki, 305-8518, Japan.</nlm:affiliation>
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<author><name sortKey="Iida, Keiko" sort="Iida, Keiko" uniqKey="Iida K" first="Keiko" last="Iida">Keiko Iida</name>
<affiliation><nlm:affiliation>Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2, Kannondai, Tsukuba, Ibaraki, 305-8518, Japan.</nlm:affiliation>
</affiliation>
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<author><name sortKey="Doi, Koji" sort="Doi, Koji" uniqKey="Doi K" first="Koji" last="Doi">Koji Doi</name>
<affiliation><nlm:affiliation>Tsukuba Gene Technology Laboratories Inc, 6-320, Arakawaoki, Tsuchiura, Ibaraki, 300-0873, Japan.</nlm:affiliation>
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<author><name sortKey="Yasue, Hiroshi" sort="Yasue, Hiroshi" uniqKey="Yasue H" first="Hiroshi" last="Yasue">Hiroshi Yasue</name>
<affiliation><nlm:affiliation>Tsukuba Gene Technology Laboratories Inc, 6-320, Arakawaoki, Tsuchiura, Ibaraki, 300-0873, Japan.</nlm:affiliation>
</affiliation>
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<series><title level="j">BMC bioinformatics</title>
<idno type="eISSN">1471-2105</idno>
<imprint><date when="2019" type="published">2019</date>
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Computational Biology (methods)</term>
<term>High-Throughput Nucleotide Sequencing</term>
<term>Polymorphism, Single Nucleotide</term>
<term>Sequence Analysis, DNA</term>
<term>Software</term>
</keywords>
<keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>High-Throughput Nucleotide Sequencing</term>
<term>Polymorphism, Single Nucleotide</term>
<term>Sequence Analysis, DNA</term>
<term>Software</term>
</keywords>
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<front><div type="abstract" xml:lang="en">Accurate detection of polymorphisms with a next generation sequencer data is an important element of current genetic analysis. However, there is still no detection pipeline that is completely reliable.</div>
</front>
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<DateCompleted><Year>2019</Year>
<Month>08</Month>
<Day>28</Day>
</DateCompleted>
<DateRevised><Year>2020</Year>
<Month>02</Month>
<Day>25</Day>
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<JournalIssue CitedMedium="Internet"><Volume>20</Volume>
<Issue>1</Issue>
<PubDate><Year>2019</Year>
<Month>Jun</Month>
<Day>28</Day>
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<Title>BMC bioinformatics</Title>
<ISOAbbreviation>BMC Bioinformatics</ISOAbbreviation>
</Journal>
<ArticleTitle>Polymorphic edge detection (PED): two efficient methods of polymorphism detection from next-generation sequencing data.</ArticleTitle>
<Pagination><MedlinePgn>362</MedlinePgn>
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<ELocationID EIdType="doi" ValidYN="Y">10.1186/s12859-019-2955-6</ELocationID>
<Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Accurate detection of polymorphisms with a next generation sequencer data is an important element of current genetic analysis. However, there is still no detection pipeline that is completely reliable.</AbstractText>
<AbstractText Label="RESULT" NlmCategory="RESULTS">We demonstrate two new detection methods of polymorphisms focusing on the Polymorphic Edge (PED). In the matching between two homologous sequences, the first mismatched base to appear is the SNP, or the edge of the structural variation. The first method is based on k-mers from short reads and detects polymorphic edges with k-mers for which there is no match between target and control, making it possible to detect SNPs by direct comparison of short-reads in two datasets (target and control) without a reference genome sequence. The second method is based on bidirectional alignment to detect polymorphic edges, not only SNPs but also insertions, deletions, inversions and translocations. Using these two methods, we succeed in making a high-quality comparison map between rice cultivars showing good match to the theoretical value of introgression, and in detecting specific large deletions across cultivars.</AbstractText>
<AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">Using Polymorphic Edge Detection (PED), the k-mer method is able to detect SNPs by direct comparison of short-reads in two datasets without genomic alignment step, and the bidirectional alignment method is able to detect SNPs and structural variations from even single-end short-reads. The PED is an efficient tool to obtain accurate data for both SNPs and structural variations.</AbstractText>
<AbstractText Label="AVAILABILITY" NlmCategory="BACKGROUND">The PED software is available at: https://github.com/akiomiyao/ped .</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Miyao</LastName>
<ForeName>Akio</ForeName>
<Initials>A</Initials>
<Identifier Source="ORCID">http://orcid.org/0000-0002-2822-2866</Identifier>
<AffiliationInfo><Affiliation>Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2, Kannondai, Tsukuba, Ibaraki, 305-8518, Japan. miyao@affrc.go.jp.</Affiliation>
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<Author ValidYN="Y"><LastName>Iida</LastName>
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<Author ValidYN="Y"><LastName>Yasue</LastName>
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<Language>eng</Language>
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<Keyword MajorTopicYN="N">Mutation</Keyword>
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Polymorphic edge detection (PED): two efficient methods of polymorphism detection from next-generation sequencing data.

Polymorphic edge detection (PED): two efficient methods of polymorphism detection from next-generation sequencing data.

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