Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Auch, Alexander F., Klenk, Hans-Peter, Göker, Markus
Formato: Texto
Lenguaje:English
Publicado: Michigan State University 2010
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
_version_ 1782197748950368256
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
work_keys_str_mv AT auchalexanderf standardoperatingprocedureforcalculatinggenometogenomedistancesbasedonhighscoringsegmentpairs
AT klenkhanspeter standardoperatingprocedureforcalculatinggenometogenomedistancesbasedonhighscoringsegmentpairs
AT gokermarkus standardoperatingprocedureforcalculatinggenometogenomedistancesbasedonhighscoringsegmentpairs