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Conference Paper: LCR_Finder: a de novo low copy repeat finder for human genome

TitleLCR_Finder: a de novo low copy repeat finder for human genome
Authors
KeywordsComplex structure
Computational tools
Genetic disease
Human chromosomes
Human genomes
Segmental duplications
Structural variations
Technical speaking
Issue Date2013
PublisherSpringer Verlag. The Journal's web site is located at http://springerlink.com/content/105633/
Citation
The 9th International Symposium on Bioinformatics Research and Applications (ISBRA 2013), Charlotte, NC., 20-22 May 2013. In Lecture Notes in Computer Science, 2013, v. 7875, p. 125-136 How to Cite?
AbstractLow copy repeats (LCRs) are reported to trigger and mediate genomic rearrangements and may result in genetic diseases. The detection of LCRs provides help to interrogate the mechanism of genetic diseases. The complex structures of LCRs render existing genomic structural variation (SV) detection and segmental duplication (SD) tools hard to predict LCR copies in full length especially those LCRs with complex SVs involved or in large scale. We developed a de novo computational tool LCR-Finder that can predict large scale (>100Kb) complex LCRs in a human genome. Technical speaking, by exploiting fast read alignment tools, LCR-Finder first generates overlapping reads from the given genome, aligns reads back to the genome to identify potential repeat regions based on multiple mapping locations. By clustering and extending these regions, we predict potential complex LCRs. We evaluated LCR-Finder on human chromosomes, we are able to identify 4 known disease related LCRs, and predict a few more possible novel LCRs. We also showed that existing tools designed for finding repeats in a genome, such RepeatScout and WindowMasker are not able to identify LCRs and tools designed for detecting SDs also cannot report large scale full length complex LCRs. © 2013 Springer-Verlag.
DescriptionLNCS v. 7875 entitled: Bioinformatics Research and Applications: 9th International Symposium, ISBRA 2013 ... : Proceedings
Persistent Identifierhttp://hdl.handle.net/10722/189636
ISBN
ISSN
2005 Impact Factor: 0.402
2015 SCImago Journal Rankings: 0.252

 

DC FieldValueLanguage
dc.contributor.authorLiu, Xen_US
dc.contributor.authorCheung, DWLen_US
dc.contributor.authorTing, HFen_US
dc.contributor.authorLam, TWen_US
dc.contributor.authorYiu, SMen_US
dc.date.accessioned2013-09-17T14:50:32Z-
dc.date.available2013-09-17T14:50:32Z-
dc.date.issued2013en_US
dc.identifier.citationThe 9th International Symposium on Bioinformatics Research and Applications (ISBRA 2013), Charlotte, NC., 20-22 May 2013. In Lecture Notes in Computer Science, 2013, v. 7875, p. 125-136en_US
dc.identifier.isbn978-364238035-8-
dc.identifier.issn0302-9743-
dc.identifier.urihttp://hdl.handle.net/10722/189636-
dc.descriptionLNCS v. 7875 entitled: Bioinformatics Research and Applications: 9th International Symposium, ISBRA 2013 ... : Proceedings-
dc.description.abstractLow copy repeats (LCRs) are reported to trigger and mediate genomic rearrangements and may result in genetic diseases. The detection of LCRs provides help to interrogate the mechanism of genetic diseases. The complex structures of LCRs render existing genomic structural variation (SV) detection and segmental duplication (SD) tools hard to predict LCR copies in full length especially those LCRs with complex SVs involved or in large scale. We developed a de novo computational tool LCR-Finder that can predict large scale (>100Kb) complex LCRs in a human genome. Technical speaking, by exploiting fast read alignment tools, LCR-Finder first generates overlapping reads from the given genome, aligns reads back to the genome to identify potential repeat regions based on multiple mapping locations. By clustering and extending these regions, we predict potential complex LCRs. We evaluated LCR-Finder on human chromosomes, we are able to identify 4 known disease related LCRs, and predict a few more possible novel LCRs. We also showed that existing tools designed for finding repeats in a genome, such RepeatScout and WindowMasker are not able to identify LCRs and tools designed for detecting SDs also cannot report large scale full length complex LCRs. © 2013 Springer-Verlag.-
dc.languageengen_US
dc.publisherSpringer Verlag. The Journal's web site is located at http://springerlink.com/content/105633/-
dc.relation.ispartofLecture Notes in Computer Scienceen_US
dc.rightsThe original publication is available at www.springerlink.com-
dc.subjectComplex structure-
dc.subjectComputational tools-
dc.subjectGenetic disease-
dc.subjectHuman chromosomes-
dc.subjectHuman genomes-
dc.subjectSegmental duplications-
dc.subjectStructural variations-
dc.subjectTechnical speaking-
dc.titleLCR_Finder: a de novo low copy repeat finder for human genomeen_US
dc.typeConference_Paperen_US
dc.identifier.emailCheung, DWL: dcheung@cs.hku.hken_US
dc.identifier.emailTing, HF: hfting@cs.hku.hken_US
dc.identifier.emailLam, TW: hresltk@hkucc.hku.hken_US
dc.identifier.emailYiu, SM: smyiu@cs.hku.hken_US
dc.identifier.authorityCheung, DWL=rp00101en_US
dc.identifier.authorityTing, HF=rp00177en_US
dc.identifier.authorityLam, TW=rp00135en_US
dc.identifier.authorityYiu, SM=rp00207en_US
dc.identifier.doi10.1007/978-3-642-38036-5_15-
dc.identifier.scopuseid_2-s2.0-84883394275-
dc.identifier.hkuros222868en_US
dc.identifier.volume7875-
dc.identifier.spage125-
dc.identifier.epage136-
dc.publisher.placeGermany-
dc.customcontrol.immutablesml 131023-

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