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Conference Paper: LCR_Finder: a de novo low copy repeat finder for human genome
Title | LCR_Finder: a de novo low copy repeat finder for human genome |
---|---|
Authors | |
Keywords | Complex structure Computational tools Genetic disease Human chromosomes Human genomes Segmental duplications Structural variations Technical speaking |
Issue Date | 2013 |
Publisher | Springer 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? |
Abstract | Low 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. |
Description | LNCS v. 7875 entitled: Bioinformatics Research and Applications: 9th International Symposium, ISBRA 2013 ... : Proceedings |
Persistent Identifier | http://hdl.handle.net/10722/189636 |
ISBN | |
ISSN | 2023 SCImago Journal Rankings: 0.606 |
DC Field | Value | Language |
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dc.contributor.author | Liu, X | en_US |
dc.contributor.author | Cheung, DWL | en_US |
dc.contributor.author | Ting, HF | en_US |
dc.contributor.author | Lam, TW | en_US |
dc.contributor.author | Yiu, SM | en_US |
dc.date.accessioned | 2013-09-17T14:50:32Z | - |
dc.date.available | 2013-09-17T14:50:32Z | - |
dc.date.issued | 2013 | en_US |
dc.identifier.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 | en_US |
dc.identifier.isbn | 978-364238035-8 | - |
dc.identifier.issn | 0302-9743 | - |
dc.identifier.uri | http://hdl.handle.net/10722/189636 | - |
dc.description | LNCS v. 7875 entitled: Bioinformatics Research and Applications: 9th International Symposium, ISBRA 2013 ... : Proceedings | - |
dc.description.abstract | Low 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.language | eng | en_US |
dc.publisher | Springer Verlag. The Journal's web site is located at http://springerlink.com/content/105633/ | - |
dc.relation.ispartof | Lecture Notes in Computer Science | en_US |
dc.rights | The original publication is available at www.springerlink.com | - |
dc.subject | Complex structure | - |
dc.subject | Computational tools | - |
dc.subject | Genetic disease | - |
dc.subject | Human chromosomes | - |
dc.subject | Human genomes | - |
dc.subject | Segmental duplications | - |
dc.subject | Structural variations | - |
dc.subject | Technical speaking | - |
dc.title | LCR_Finder: a de novo low copy repeat finder for human genome | en_US |
dc.type | Conference_Paper | en_US |
dc.identifier.email | Cheung, DWL: dcheung@cs.hku.hk | en_US |
dc.identifier.email | Ting, HF: hfting@cs.hku.hk | en_US |
dc.identifier.email | Lam, TW: hresltk@hkucc.hku.hk | en_US |
dc.identifier.email | Yiu, SM: smyiu@cs.hku.hk | en_US |
dc.identifier.authority | Cheung, DWL=rp00101 | en_US |
dc.identifier.authority | Ting, HF=rp00177 | en_US |
dc.identifier.authority | Lam, TW=rp00135 | en_US |
dc.identifier.authority | Yiu, SM=rp00207 | en_US |
dc.identifier.doi | 10.1007/978-3-642-38036-5_15 | - |
dc.identifier.scopus | eid_2-s2.0-84883394275 | - |
dc.identifier.hkuros | 222868 | en_US |
dc.identifier.volume | 7875 | - |
dc.identifier.spage | 125 | - |
dc.identifier.epage | 136 | - |
dc.publisher.place | Germany | - |
dc.customcontrol.immutable | sml 131023 | - |
dc.identifier.issnl | 0302-9743 | - |