BAGET 2.0: an updated web tool for the effortless retrieval of prokaryotic gene context and sequence

MOTIVATION: The retrieval of a single gene sequence and context from completely sequenced bacterial and archaeal genomes constitutes an intimidating task for the wet bench biologist. Existing web-based genome browsers are either too complex for routine use or only provide a subset of the available p...

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Detalles Bibliográficos
Autores principales: Hepp, Benjamin, Da Cunha, Violette, Lorieux, Florence, Oberto, Jacques
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8428571/
https://www.ncbi.nlm.nih.gov/pubmed/33532841
http://dx.doi.org/10.1093/bioinformatics/btab082
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author Hepp, Benjamin
Da Cunha, Violette
Lorieux, Florence
Oberto, Jacques
author_facet Hepp, Benjamin
Da Cunha, Violette
Lorieux, Florence
Oberto, Jacques
author_sort Hepp, Benjamin
collection PubMed
description MOTIVATION: The retrieval of a single gene sequence and context from completely sequenced bacterial and archaeal genomes constitutes an intimidating task for the wet bench biologist. Existing web-based genome browsers are either too complex for routine use or only provide a subset of the available prokaryotic genomes. RESULTS: We have developed BAGET 2.0 (Bacterial and Archaeal Gene Exploration Tool), an updated web service granting access in just three mouse clicks to the sequence and synteny of any gene from completely sequenced bacteria and archaea. User-provided annotated genomes can be processed as well. BAGET 2.0 relies on a local database updated on a daily basis. AVAILABILITY AND IMPLEMENTATION: BAGET 2.0 befits all current browsers such as Chrome, Firefox, Edge, Opera and Safari. Internet Explorer 11 is supported. BAGET 2.0 is freely accessible at https://archaea.i2bc.paris-saclay.fr/baget/
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spelling pubmed-84285712021-09-10 BAGET 2.0: an updated web tool for the effortless retrieval of prokaryotic gene context and sequence Hepp, Benjamin Da Cunha, Violette Lorieux, Florence Oberto, Jacques Bioinformatics Applications Notes MOTIVATION: The retrieval of a single gene sequence and context from completely sequenced bacterial and archaeal genomes constitutes an intimidating task for the wet bench biologist. Existing web-based genome browsers are either too complex for routine use or only provide a subset of the available prokaryotic genomes. RESULTS: We have developed BAGET 2.0 (Bacterial and Archaeal Gene Exploration Tool), an updated web service granting access in just three mouse clicks to the sequence and synteny of any gene from completely sequenced bacteria and archaea. User-provided annotated genomes can be processed as well. BAGET 2.0 relies on a local database updated on a daily basis. AVAILABILITY AND IMPLEMENTATION: BAGET 2.0 befits all current browsers such as Chrome, Firefox, Edge, Opera and Safari. Internet Explorer 11 is supported. BAGET 2.0 is freely accessible at https://archaea.i2bc.paris-saclay.fr/baget/ Oxford University Press 2021-02-03 /pmc/articles/PMC8428571/ /pubmed/33532841 http://dx.doi.org/10.1093/bioinformatics/btab082 Text en © The Author(s) 2021. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Notes
Hepp, Benjamin
Da Cunha, Violette
Lorieux, Florence
Oberto, Jacques
BAGET 2.0: an updated web tool for the effortless retrieval of prokaryotic gene context and sequence
title BAGET 2.0: an updated web tool for the effortless retrieval of prokaryotic gene context and sequence
title_full BAGET 2.0: an updated web tool for the effortless retrieval of prokaryotic gene context and sequence
title_fullStr BAGET 2.0: an updated web tool for the effortless retrieval of prokaryotic gene context and sequence
title_full_unstemmed BAGET 2.0: an updated web tool for the effortless retrieval of prokaryotic gene context and sequence
title_short BAGET 2.0: an updated web tool for the effortless retrieval of prokaryotic gene context and sequence
title_sort baget 2.0: an updated web tool for the effortless retrieval of prokaryotic gene context and sequence
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8428571/
https://www.ncbi.nlm.nih.gov/pubmed/33532841
http://dx.doi.org/10.1093/bioinformatics/btab082
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