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Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs
DNA-DNA hybridization (DDH) is a widely applied wet-lab technique to obtain an estimate of the overall similarity between the genomes of two organisms. To base the species concept for prokaryotes ultimately on DDH was chosen by microbiologists as a pragmatic approach for deciding about the recogniti...
Autores principales: | , , |
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Formato: | Texto |
Lenguaje: | English |
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Michigan State University
2010
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3035261/ https://www.ncbi.nlm.nih.gov/pubmed/21304686 http://dx.doi.org/10.4056/sigs.541628 |
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author | Auch, Alexander F. Klenk, Hans-Peter Göker, Markus |
author_facet | Auch, Alexander F. Klenk, Hans-Peter Göker, Markus |
author_sort | Auch, Alexander F. |
collection | PubMed |
description | DNA-DNA hybridization (DDH) is a widely applied wet-lab technique to obtain an estimate of the overall similarity between the genomes of two organisms. To base the species concept for prokaryotes ultimately on DDH was chosen by microbiologists as a pragmatic approach for deciding about the recognition of novel species, but also allowed a relatively high degree of standardization compared to other areas of taxonomy. However, DDH is tedious and error-prone and first and foremost cannot be used to incrementally establish a comparative database. Recent studies have shown that in-silico methods for the comparison of genome sequences can be used to replace DDH. Considering the ongoing rapid technological progress of sequencing methods, genome-based prokaryote taxonomy is coming into reach. However, calculating distances between genomes is dependent on multiple choices for software and program settings. We here provide an overview over the modifications that can be applied to distance methods based in high-scoring segment pairs (HSPs) or maximally unique matches (MUMs) and that need to be documented. General recommendations on determining HSPs using BLAST or other algorithms are also provided. As a reference implementation, we introduce the GGDC web server (http://ggdc.gbdp.org). |
format | Text |
id | pubmed-3035261 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2010 |
publisher | Michigan State University |
record_format | MEDLINE/PubMed |
spelling | pubmed-30352612011-02-08 Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs Auch, Alexander F. Klenk, Hans-Peter Göker, Markus Stand Genomic Sci Standard Operating Procedures DNA-DNA hybridization (DDH) is a widely applied wet-lab technique to obtain an estimate of the overall similarity between the genomes of two organisms. To base the species concept for prokaryotes ultimately on DDH was chosen by microbiologists as a pragmatic approach for deciding about the recognition of novel species, but also allowed a relatively high degree of standardization compared to other areas of taxonomy. However, DDH is tedious and error-prone and first and foremost cannot be used to incrementally establish a comparative database. Recent studies have shown that in-silico methods for the comparison of genome sequences can be used to replace DDH. Considering the ongoing rapid technological progress of sequencing methods, genome-based prokaryote taxonomy is coming into reach. However, calculating distances between genomes is dependent on multiple choices for software and program settings. We here provide an overview over the modifications that can be applied to distance methods based in high-scoring segment pairs (HSPs) or maximally unique matches (MUMs) and that need to be documented. General recommendations on determining HSPs using BLAST or other algorithms are also provided. As a reference implementation, we introduce the GGDC web server (http://ggdc.gbdp.org). Michigan State University 2010-01-28 /pmc/articles/PMC3035261/ /pubmed/21304686 http://dx.doi.org/10.4056/sigs.541628 Text en http://creativecommons.org/licenses/by/2.5/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Standard Operating Procedures Auch, Alexander F. Klenk, Hans-Peter Göker, Markus Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs |
title | Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs |
title_full | Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs |
title_fullStr | Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs |
title_full_unstemmed | Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs |
title_short | Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs |
title_sort | standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs |
topic | Standard Operating Procedures |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3035261/ https://www.ncbi.nlm.nih.gov/pubmed/21304686 http://dx.doi.org/10.4056/sigs.541628 |
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