Fast characterization of segmental duplications in genome assemblies
Segmental duplications (SDs) or low-copy repeats, are segments of DNA > 1 Kbp with high sequence identity that are copied to other regions of the genome. SDs are among the most important sources of evolution, a common cause of genomic structural variation and several are associated with diseases...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Oxford University Press
2019
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| Online Access: | https://hdl.handle.net/1721.1/122936 |
| _version_ | 1826188719482208256 |
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| author | Numanagic, Ibrahim Gokkaya, Alim S. Zhang, Lillian Berger Leighton, Bonnie Alkan, Can Hach, Faraz |
| author2 | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory |
| author_facet | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory Numanagic, Ibrahim Gokkaya, Alim S. Zhang, Lillian Berger Leighton, Bonnie Alkan, Can Hach, Faraz |
| author_sort | Numanagic, Ibrahim |
| collection | MIT |
| description | Segmental duplications (SDs) or low-copy repeats, are segments of DNA > 1 Kbp with high sequence identity that are copied to other regions of the genome. SDs are among the most important sources of evolution, a common cause of genomic structural variation and several are associated with diseases of genomic origin including schizophrenia and autism. Despite their functional importance, SDs present one of the major hurdles for de novo genome assembly due to the ambiguity they cause in building and traversing both state-of-the-art overlap-layout-consensus and de Bruijn graphs. This causes SD regions to be misassembled, collapsed into a unique representation, or completely missing from assembled reference genomes for various organisms. In turn, this missing or incorrect information limits our ability to fully understand the evolution and the architecture of the genomes. Despite the essential need to accurately characterize SDs in assemblies, there has been only one tool that was developed for this purpose, called Whole-Genome Assembly Comparison (WGAC); its primary goal is SD detection. WGAC is comprised of several steps that employ different tools and custom scripts, which makes this strategy difficult and time consuming to use. Thus there is still a need for algorithms to characterize within-assembly SDs quickly, accurately, and in a user friendly manner. |
| first_indexed | 2024-09-23T08:03:58Z |
| format | Article |
| id | mit-1721.1/122936 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T08:03:58Z |
| publishDate | 2019 |
| publisher | Oxford University Press |
| record_format | dspace |
| spelling | mit-1721.1/1229362022-09-23T10:39:23Z Fast characterization of segmental duplications in genome assemblies Numanagic, Ibrahim Gokkaya, Alim S. Zhang, Lillian Berger Leighton, Bonnie Alkan, Can Hach, Faraz Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology. Department of Mathematics Segmental duplications (SDs) or low-copy repeats, are segments of DNA > 1 Kbp with high sequence identity that are copied to other regions of the genome. SDs are among the most important sources of evolution, a common cause of genomic structural variation and several are associated with diseases of genomic origin including schizophrenia and autism. Despite their functional importance, SDs present one of the major hurdles for de novo genome assembly due to the ambiguity they cause in building and traversing both state-of-the-art overlap-layout-consensus and de Bruijn graphs. This causes SD regions to be misassembled, collapsed into a unique representation, or completely missing from assembled reference genomes for various organisms. In turn, this missing or incorrect information limits our ability to fully understand the evolution and the architecture of the genomes. Despite the essential need to accurately characterize SDs in assemblies, there has been only one tool that was developed for this purpose, called Whole-Genome Assembly Comparison (WGAC); its primary goal is SD detection. WGAC is comprised of several steps that employ different tools and custom scripts, which makes this strategy difficult and time consuming to use. Thus there is still a need for algorithms to characterize within-assembly SDs quickly, accurately, and in a user friendly manner. National Institutes of Health (U.S.) (Grant GM108348) 2019-11-14T18:34:48Z 2019-11-14T18:34:48Z 2018-09-08 2019-11-07T18:38:22Z Article http://purl.org/eprint/type/JournalArticle 1367-4803 1460-2059 https://hdl.handle.net/1721.1/122936 Numanagic, Ibrahim et al. "Fast characterization of segmental duplications in genome assemblies." Bioinformatics 34, 17 (2018) : i706–i714 © 2018 The Author(s) en http://dx.doi.org/10.1093/bioinformatics/bty586 Bioinformatics Creative Commons Attribution NonCommercial License 4.0 https://creativecommons.org/licenses/by-nc/4.0/ application/pdf Oxford University Press Oxford University Press |
| spellingShingle | Numanagic, Ibrahim Gokkaya, Alim S. Zhang, Lillian Berger Leighton, Bonnie Alkan, Can Hach, Faraz Fast characterization of segmental duplications in genome assemblies |
| title | Fast characterization of segmental duplications in genome assemblies |
| title_full | Fast characterization of segmental duplications in genome assemblies |
| title_fullStr | Fast characterization of segmental duplications in genome assemblies |
| title_full_unstemmed | Fast characterization of segmental duplications in genome assemblies |
| title_short | Fast characterization of segmental duplications in genome assemblies |
| title_sort | fast characterization of segmental duplications in genome assemblies |
| url | https://hdl.handle.net/1721.1/122936 |
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