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Sequence, a BioJS component for visualising sequences

Summary: Sequences are probably the most common piece of information in sites providing biological data resources, particularly those related to genes and proteins. Multiple visual representations of the same sequence can be found across those sites. This can lead to an inconsistency compromising bo...

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Detalles Bibliográficos
Autores principales: Gomez, John, Jimenez, Rafael
Formato: Online Artículo Texto
Lenguaje:English
Publicado: F1000Research 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4103491/
https://www.ncbi.nlm.nih.gov/pubmed/25075289
http://dx.doi.org/10.12688/f1000research.3-52.v1
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author Gomez, John
Jimenez, Rafael
author_facet Gomez, John
Jimenez, Rafael
author_sort Gomez, John
collection PubMed
description Summary: Sequences are probably the most common piece of information in sites providing biological data resources, particularly those related to genes and proteins. Multiple visual representations of the same sequence can be found across those sites. This can lead to an inconsistency compromising both the user experience and usability while working with graphical representations of a sequence. Furthermore, the code of the visualisation module is commonly embedded and merged with the rest of the application, making it difficult to reuse it in other applications. In this paper, we present a BioJS component for visualising sequences with a set of options supporting a flexible configuration of the visual representation, such as formats, colours, annotations, and columns, among others. This component aims to facilitate a common representation across different sites, making it easier for end users to move from one site to another. Availability: http://www.ebi.ac.uk/Tools/biojs; http://dx.doi.org/10.5281/zenodo.8299
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spelling pubmed-41034912014-07-28 Sequence, a BioJS component for visualising sequences Gomez, John Jimenez, Rafael F1000Res Web Tool Summary: Sequences are probably the most common piece of information in sites providing biological data resources, particularly those related to genes and proteins. Multiple visual representations of the same sequence can be found across those sites. This can lead to an inconsistency compromising both the user experience and usability while working with graphical representations of a sequence. Furthermore, the code of the visualisation module is commonly embedded and merged with the rest of the application, making it difficult to reuse it in other applications. In this paper, we present a BioJS component for visualising sequences with a set of options supporting a flexible configuration of the visual representation, such as formats, colours, annotations, and columns, among others. This component aims to facilitate a common representation across different sites, making it easier for end users to move from one site to another. Availability: http://www.ebi.ac.uk/Tools/biojs; http://dx.doi.org/10.5281/zenodo.8299 F1000Research 2014-02-13 /pmc/articles/PMC4103491/ /pubmed/25075289 http://dx.doi.org/10.12688/f1000research.3-52.v1 Text en Copyright: © 2014 Gomez J and Jimenez R http://creativecommons.org/licenses/by/3.0/ This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. http://creativecommons.org/publicdomain/zero/1.0/ Data associated with the article are available under the terms of the Creative Commons Zero "No rights reserved" data waiver (CC0 1.0 Public domain dedication).
spellingShingle Web Tool
Gomez, John
Jimenez, Rafael
Sequence, a BioJS component for visualising sequences
title Sequence, a BioJS component for visualising sequences
title_full Sequence, a BioJS component for visualising sequences
title_fullStr Sequence, a BioJS component for visualising sequences
title_full_unstemmed Sequence, a BioJS component for visualising sequences
title_short Sequence, a BioJS component for visualising sequences
title_sort sequence, a biojs component for visualising sequences
topic Web Tool
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4103491/
https://www.ncbi.nlm.nih.gov/pubmed/25075289
http://dx.doi.org/10.12688/f1000research.3-52.v1
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