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Defining objective clusters for rabies virus sequences using affinity propagation clustering

Rabies is caused by lyssaviruses, and is one of the oldest known zoonoses. In recent years, more than 21,000 nucleotide sequences of rabies viruses (RABV), from the prototype species rabies lyssavirus, have been deposited in public databases. Subsequent phylogenetic analyses in combination with meta...

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Autores principales: Fischer, Susanne, Freuling, Conrad M., Müller, Thomas, Pfaff, Florian, Bodenhofer, Ulrich, Höper, Dirk, Fischer, Mareike, Marston, Denise A., Fooks, Anthony R., Mettenleiter, Thomas C., Conraths, Franz J., Homeier-Bachmann, Timo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5794188/
https://www.ncbi.nlm.nih.gov/pubmed/29357361
http://dx.doi.org/10.1371/journal.pntd.0006182
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author Fischer, Susanne
Freuling, Conrad M.
Müller, Thomas
Pfaff, Florian
Bodenhofer, Ulrich
Höper, Dirk
Fischer, Mareike
Marston, Denise A.
Fooks, Anthony R.
Mettenleiter, Thomas C.
Conraths, Franz J.
Homeier-Bachmann, Timo
author_facet Fischer, Susanne
Freuling, Conrad M.
Müller, Thomas
Pfaff, Florian
Bodenhofer, Ulrich
Höper, Dirk
Fischer, Mareike
Marston, Denise A.
Fooks, Anthony R.
Mettenleiter, Thomas C.
Conraths, Franz J.
Homeier-Bachmann, Timo
author_sort Fischer, Susanne
collection PubMed
description Rabies is caused by lyssaviruses, and is one of the oldest known zoonoses. In recent years, more than 21,000 nucleotide sequences of rabies viruses (RABV), from the prototype species rabies lyssavirus, have been deposited in public databases. Subsequent phylogenetic analyses in combination with metadata suggest geographic distributions of RABV. However, these analyses somewhat experience technical difficulties in defining verifiable criteria for cluster allocations in phylogenetic trees inviting for a more rational approach. Therefore, we applied a relatively new mathematical clustering algorythm named ‘affinity propagation clustering’ (AP) to propose a standardized sub-species classification utilizing full-genome RABV sequences. Because AP has the advantage that it is computationally fast and works for any meaningful measure of similarity between data samples, it has previously been applied successfully in bioinformatics, for analysis of microarray and gene expression data, however, cluster analysis of sequences is still in its infancy. Existing (516) and original (46) full genome RABV sequences were used to demonstrate the application of AP for RABV clustering. On a global scale, AP proposed four clusters, i.e. New World cluster, Arctic/Arctic-like, Cosmopolitan, and Asian as previously assigned by phylogenetic studies. By combining AP with established phylogenetic analyses, it is possible to resolve phylogenetic relationships between verifiably determined clusters and sequences. This workflow will be useful in confirming cluster distributions in a uniform transparent manner, not only for RABV, but also for other comparative sequence analyses.
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spelling pubmed-57941882018-02-16 Defining objective clusters for rabies virus sequences using affinity propagation clustering Fischer, Susanne Freuling, Conrad M. Müller, Thomas Pfaff, Florian Bodenhofer, Ulrich Höper, Dirk Fischer, Mareike Marston, Denise A. Fooks, Anthony R. Mettenleiter, Thomas C. Conraths, Franz J. Homeier-Bachmann, Timo PLoS Negl Trop Dis Research Article Rabies is caused by lyssaviruses, and is one of the oldest known zoonoses. In recent years, more than 21,000 nucleotide sequences of rabies viruses (RABV), from the prototype species rabies lyssavirus, have been deposited in public databases. Subsequent phylogenetic analyses in combination with metadata suggest geographic distributions of RABV. However, these analyses somewhat experience technical difficulties in defining verifiable criteria for cluster allocations in phylogenetic trees inviting for a more rational approach. Therefore, we applied a relatively new mathematical clustering algorythm named ‘affinity propagation clustering’ (AP) to propose a standardized sub-species classification utilizing full-genome RABV sequences. Because AP has the advantage that it is computationally fast and works for any meaningful measure of similarity between data samples, it has previously been applied successfully in bioinformatics, for analysis of microarray and gene expression data, however, cluster analysis of sequences is still in its infancy. Existing (516) and original (46) full genome RABV sequences were used to demonstrate the application of AP for RABV clustering. On a global scale, AP proposed four clusters, i.e. New World cluster, Arctic/Arctic-like, Cosmopolitan, and Asian as previously assigned by phylogenetic studies. By combining AP with established phylogenetic analyses, it is possible to resolve phylogenetic relationships between verifiably determined clusters and sequences. This workflow will be useful in confirming cluster distributions in a uniform transparent manner, not only for RABV, but also for other comparative sequence analyses. Public Library of Science 2018-01-22 /pmc/articles/PMC5794188/ /pubmed/29357361 http://dx.doi.org/10.1371/journal.pntd.0006182 Text en © 2018 Fischer et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Fischer, Susanne
Freuling, Conrad M.
Müller, Thomas
Pfaff, Florian
Bodenhofer, Ulrich
Höper, Dirk
Fischer, Mareike
Marston, Denise A.
Fooks, Anthony R.
Mettenleiter, Thomas C.
Conraths, Franz J.
Homeier-Bachmann, Timo
Defining objective clusters for rabies virus sequences using affinity propagation clustering
title Defining objective clusters for rabies virus sequences using affinity propagation clustering
title_full Defining objective clusters for rabies virus sequences using affinity propagation clustering
title_fullStr Defining objective clusters for rabies virus sequences using affinity propagation clustering
title_full_unstemmed Defining objective clusters for rabies virus sequences using affinity propagation clustering
title_short Defining objective clusters for rabies virus sequences using affinity propagation clustering
title_sort defining objective clusters for rabies virus sequences using affinity propagation clustering
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5794188/
https://www.ncbi.nlm.nih.gov/pubmed/29357361
http://dx.doi.org/10.1371/journal.pntd.0006182
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