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  Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads

Sun, R., Love, M., Zemojtel, T., Emde, A.-K., Chung, H.-R., Vingron, M., et al. (2012). Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads. Bioinformatics, 28(7), 1024-1025. doi:10.1093/bioinformatics/bts064.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0014-7B7B-B Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0014-7B9F-C
Genre: Journal Article

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 Creators:
Sun, Ruping1, Author              
Love, Michael2, Author              
Zemojtel, Tomas3, Author              
Emde, Anne-Katrin1, Author              
Chung, Ho-Ryun4, Author              
Vingron, Martin5, Author              
Haas, Stefan1, Author              
Affiliations:
1Gene Structure and Array Design (Stefan Haas), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, Ihnestr. 73, 14195 Berlin, ou_1479640              
2IMPRS for Computational Biology and Scientific Computing - IMPRS-CBSC (Kirsten Kelleher), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, Ihnestr, 73, 14195 Berlin, ou_1479666              
3Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, Ihnestr, 73, 14195 Berlin, ou_1433547              
4Computational Epigenetics (Ho-Ryun Chung), Independent Junior Research Groups (OWL), Max Planck Institute for Molecular Genetics, Max Planck Society, Ihnestr, 73, 14195 Berlin, ou_1479658              
5Gene regulation (Martin Vingron), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, Ihnestr, 73, 14195 Berlin, ou_1479639              

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 Abstract: Summary: We developed Breakpointer, a fast algorithm to locate breakpoints of structural variants (SVs) from single-end reads produced by next-generation sequencing. By taking advantage of local non-uniform read distribution and misalignments created by SVs, Breakpointer scans the alignment of single-end reads to identify regions containing potential breakpoints. The detection of such breakpoints can indicate insertions longer than the read length and SVs located in repetitve regions which might be missd by other methods. Thus, Breakpointer complements existing methods to locate SVs from single-end reads.Availability: https://github.com/ruping/BreakpointerContact: ruping@molgen.mpg.deSupplementary information: Supplementary material is available at Bioinformatics online.

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Language(s): eng - English
 Dates: 2012
 Publication Status: Published in print
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 Rev. Method: Peer
 Identifiers: DOI: 10.1093/bioinformatics/bts064
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Title: Bioinformatics
Source Genre: Journal
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Publ. Info: Oxford : Oxford University Press
Pages: - Volume / Issue: 28 (7) Sequence Number: - Start / End Page: 1024 - 1025 Identifier: ISSN: 1367-4803
CoNE: https://pure.mpg.de/cone/journals/resource/954926969991