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WASPS: web-assisted symbolic plasmid synteny server
MOTIVATION: Comparative plasmid genome analyses require complex tools, the manipulation of large numbers of sequences and constitute a daunting task for the wet bench experimentalist. Dedicated plasmid databases are sparse, only comprise bacterial plasmids and provide exclusively access to sequence...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7703779/ https://www.ncbi.nlm.nih.gov/pubmed/31589313 http://dx.doi.org/10.1093/bioinformatics/btz745 |
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author | Badel, Catherine Da Cunha, Violette Catchpole, Ryan Forterre, Patrick Oberto, Jacques |
author_facet | Badel, Catherine Da Cunha, Violette Catchpole, Ryan Forterre, Patrick Oberto, Jacques |
author_sort | Badel, Catherine |
collection | PubMed |
description | MOTIVATION: Comparative plasmid genome analyses require complex tools, the manipulation of large numbers of sequences and constitute a daunting task for the wet bench experimentalist. Dedicated plasmid databases are sparse, only comprise bacterial plasmids and provide exclusively access to sequence similarity searches. RESULTS: We have developed Web-Assisted Symbolic Plasmid Synteny (WASPS), a web service granting protein and DNA sequence similarity searches against a database comprising all completely sequenced natural plasmids from bacterial, archaeal and eukaryal origin. This database pre-calculates orthologous protein clustering and enables WASPS to generate fully resolved plasmid synteny maps in real time using internal and user-provided DNA sequences. AVAILABILITY AND IMPLEMENTATION: WASPS queries befit all current browsers such as Firefox, Edge or Safari while the best functionality is achieved with Chrome. Internet Explorer is not supported. WASPS is freely accessible at https://archaea.i2bc.paris-saclay.fr/wasps/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. |
format | Online Article Text |
id | pubmed-7703779 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-77037792020-12-07 WASPS: web-assisted symbolic plasmid synteny server Badel, Catherine Da Cunha, Violette Catchpole, Ryan Forterre, Patrick Oberto, Jacques Bioinformatics Applications Note MOTIVATION: Comparative plasmid genome analyses require complex tools, the manipulation of large numbers of sequences and constitute a daunting task for the wet bench experimentalist. Dedicated plasmid databases are sparse, only comprise bacterial plasmids and provide exclusively access to sequence similarity searches. RESULTS: We have developed Web-Assisted Symbolic Plasmid Synteny (WASPS), a web service granting protein and DNA sequence similarity searches against a database comprising all completely sequenced natural plasmids from bacterial, archaeal and eukaryal origin. This database pre-calculates orthologous protein clustering and enables WASPS to generate fully resolved plasmid synteny maps in real time using internal and user-provided DNA sequences. AVAILABILITY AND IMPLEMENTATION: WASPS queries befit all current browsers such as Firefox, Edge or Safari while the best functionality is achieved with Chrome. Internet Explorer is not supported. WASPS is freely accessible at https://archaea.i2bc.paris-saclay.fr/wasps/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2020-03 2019-10-07 /pmc/articles/PMC7703779/ /pubmed/31589313 http://dx.doi.org/10.1093/bioinformatics/btz745 Text en © The Author(s) 2019. Published by Oxford University Press. 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 | Applications Note Badel, Catherine Da Cunha, Violette Catchpole, Ryan Forterre, Patrick Oberto, Jacques WASPS: web-assisted symbolic plasmid synteny server |
title | WASPS: web-assisted symbolic plasmid synteny server |
title_full | WASPS: web-assisted symbolic plasmid synteny server |
title_fullStr | WASPS: web-assisted symbolic plasmid synteny server |
title_full_unstemmed | WASPS: web-assisted symbolic plasmid synteny server |
title_short | WASPS: web-assisted symbolic plasmid synteny server |
title_sort | wasps: web-assisted symbolic plasmid synteny server |
topic | Applications Note |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7703779/ https://www.ncbi.nlm.nih.gov/pubmed/31589313 http://dx.doi.org/10.1093/bioinformatics/btz745 |
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