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IAMBEE: a web-service for the identification of adaptive pathways from parallel evolved clonal populations
IAMBEE is a web server designed for the Identification of Adaptive Mutations in Bacterial Evolution Experiments (IAMBEE). Input data consist of genotype information obtained from independently evolved clonal populations or strains that show the same adapted behavior (phenotype). To distinguish adapt...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6602435/ https://www.ncbi.nlm.nih.gov/pubmed/31127271 http://dx.doi.org/10.1093/nar/gkz451 |
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author | Perez-Romero, Camilo Andres Weytjens, Bram Decap, Dries Swings, Toon Michiels, Jan De Maeyer, Dries Marchal, Kathleen |
author_facet | Perez-Romero, Camilo Andres Weytjens, Bram Decap, Dries Swings, Toon Michiels, Jan De Maeyer, Dries Marchal, Kathleen |
author_sort | Perez-Romero, Camilo Andres |
collection | PubMed |
description | IAMBEE is a web server designed for the Identification of Adaptive Mutations in Bacterial Evolution Experiments (IAMBEE). Input data consist of genotype information obtained from independently evolved clonal populations or strains that show the same adapted behavior (phenotype). To distinguish adaptive from passenger mutations, IAMBEE searches for neighborhoods in an organism-specific interaction network that are recurrently mutated in the adapted populations. This search for recurrently mutated network neighborhoods, as proxies for pathways is driven by additional information on the functional impact of the observed genetic changes and their dynamics during adaptive evolution. In addition, the search explicitly accounts for the differences in mutation rate between the independently evolved populations. Using this approach, IAMBEE allows exploiting parallel evolution to identify adaptive pathways. The web-server is freely available at http://bioinformatics.intec.ugent.be/iambee/ with no login requirement. |
format | Online Article Text |
id | pubmed-6602435 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-66024352019-07-05 IAMBEE: a web-service for the identification of adaptive pathways from parallel evolved clonal populations Perez-Romero, Camilo Andres Weytjens, Bram Decap, Dries Swings, Toon Michiels, Jan De Maeyer, Dries Marchal, Kathleen Nucleic Acids Res Web Server Issue IAMBEE is a web server designed for the Identification of Adaptive Mutations in Bacterial Evolution Experiments (IAMBEE). Input data consist of genotype information obtained from independently evolved clonal populations or strains that show the same adapted behavior (phenotype). To distinguish adaptive from passenger mutations, IAMBEE searches for neighborhoods in an organism-specific interaction network that are recurrently mutated in the adapted populations. This search for recurrently mutated network neighborhoods, as proxies for pathways is driven by additional information on the functional impact of the observed genetic changes and their dynamics during adaptive evolution. In addition, the search explicitly accounts for the differences in mutation rate between the independently evolved populations. Using this approach, IAMBEE allows exploiting parallel evolution to identify adaptive pathways. The web-server is freely available at http://bioinformatics.intec.ugent.be/iambee/ with no login requirement. Oxford University Press 2019-07-02 2019-05-25 /pmc/articles/PMC6602435/ /pubmed/31127271 http://dx.doi.org/10.1093/nar/gkz451 Text en © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Web Server Issue Perez-Romero, Camilo Andres Weytjens, Bram Decap, Dries Swings, Toon Michiels, Jan De Maeyer, Dries Marchal, Kathleen IAMBEE: a web-service for the identification of adaptive pathways from parallel evolved clonal populations |
title | IAMBEE: a web-service for the identification of adaptive pathways from parallel evolved clonal populations |
title_full | IAMBEE: a web-service for the identification of adaptive pathways from parallel evolved clonal populations |
title_fullStr | IAMBEE: a web-service for the identification of adaptive pathways from parallel evolved clonal populations |
title_full_unstemmed | IAMBEE: a web-service for the identification of adaptive pathways from parallel evolved clonal populations |
title_short | IAMBEE: a web-service for the identification of adaptive pathways from parallel evolved clonal populations |
title_sort | iambee: a web-service for the identification of adaptive pathways from parallel evolved clonal populations |
topic | Web Server Issue |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6602435/ https://www.ncbi.nlm.nih.gov/pubmed/31127271 http://dx.doi.org/10.1093/nar/gkz451 |
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