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Old can be new again: HAPPY whole genome sequencing, mapping and assembly
During the last three decades, both genome mapping and sequencing methods have advanced significantly to provide a foundation for scientists to understand genome structures and functions in many species. Generally speaking, genome mapping relies on genome sequencing to provide basic materials, such...
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Formato: | Texto |
Lenguaje: | English |
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Ivyspring International Publisher
2009
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2669597/ https://www.ncbi.nlm.nih.gov/pubmed/19381348 |
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author | Jiang, Zhihua Rokhsar, Daniel S. Harland, Richard M. |
author_facet | Jiang, Zhihua Rokhsar, Daniel S. Harland, Richard M. |
author_sort | Jiang, Zhihua |
collection | PubMed |
description | During the last three decades, both genome mapping and sequencing methods have advanced significantly to provide a foundation for scientists to understand genome structures and functions in many species. Generally speaking, genome mapping relies on genome sequencing to provide basic materials, such as DNA probes and markers for their localizations, thus constructing the maps. On the other hand, genome sequencing often requires a high-resolution map as a skeleton for whole genome assembly. However, both genome mapping and sequencing have never come together in one pipeline. After reviewing mapping and next-generation sequencing methods, we would like to share our thoughts with the genome community on how to combine the HAPPY mapping technique with the new-generation sequencing, thus integrating two systems into one pipeline, called HAPPY pipeline. The pipeline starts with preparation of a HAPPY panel, followed by multiple displacement amplification for producing a relatively large quantity of DNA. Instead of conventional marker genotyping, the amplified panel DNA samples are subject to new-generation sequencing with barcode method, which allows us to determine the presence/absence of a sequence contig as a traditional marker in the HAPPY panel. Statistical analysis will then be performed to infer how close or how far away from each other these contigs are within a genome and order the whole genome sequence assembly as well. We believe that such a universal approach will play an important role in genome sequencing, mapping, and assembly of many species; thus advancing genome science and its applications in biomedicine and agriculture. |
format | Text |
id | pubmed-2669597 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2009 |
publisher | Ivyspring International Publisher |
record_format | MEDLINE/PubMed |
spelling | pubmed-26695972009-04-16 Old can be new again: HAPPY whole genome sequencing, mapping and assembly Jiang, Zhihua Rokhsar, Daniel S. Harland, Richard M. Int J Biol Sci Review During the last three decades, both genome mapping and sequencing methods have advanced significantly to provide a foundation for scientists to understand genome structures and functions in many species. Generally speaking, genome mapping relies on genome sequencing to provide basic materials, such as DNA probes and markers for their localizations, thus constructing the maps. On the other hand, genome sequencing often requires a high-resolution map as a skeleton for whole genome assembly. However, both genome mapping and sequencing have never come together in one pipeline. After reviewing mapping and next-generation sequencing methods, we would like to share our thoughts with the genome community on how to combine the HAPPY mapping technique with the new-generation sequencing, thus integrating two systems into one pipeline, called HAPPY pipeline. The pipeline starts with preparation of a HAPPY panel, followed by multiple displacement amplification for producing a relatively large quantity of DNA. Instead of conventional marker genotyping, the amplified panel DNA samples are subject to new-generation sequencing with barcode method, which allows us to determine the presence/absence of a sequence contig as a traditional marker in the HAPPY panel. Statistical analysis will then be performed to infer how close or how far away from each other these contigs are within a genome and order the whole genome sequence assembly as well. We believe that such a universal approach will play an important role in genome sequencing, mapping, and assembly of many species; thus advancing genome science and its applications in biomedicine and agriculture. Ivyspring International Publisher 2009-04-15 /pmc/articles/PMC2669597/ /pubmed/19381348 Text en © Ivyspring International Publisher. This is an open-access article distributed under the terms of the Creative Commons License (http://creativecommons.org/licenses/by-nc-nd/3.0/). Reproduction is permitted for personal, noncommercial use, provided that the article is in whole, unmodified, and properly cited. |
spellingShingle | Review Jiang, Zhihua Rokhsar, Daniel S. Harland, Richard M. Old can be new again: HAPPY whole genome sequencing, mapping and assembly |
title | Old can be new again: HAPPY whole genome sequencing, mapping and assembly |
title_full | Old can be new again: HAPPY whole genome sequencing, mapping and assembly |
title_fullStr | Old can be new again: HAPPY whole genome sequencing, mapping and assembly |
title_full_unstemmed | Old can be new again: HAPPY whole genome sequencing, mapping and assembly |
title_short | Old can be new again: HAPPY whole genome sequencing, mapping and assembly |
title_sort | old can be new again: happy whole genome sequencing, mapping and assembly |
topic | Review |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2669597/ https://www.ncbi.nlm.nih.gov/pubmed/19381348 |
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