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blastjs: a BLAST+ wrapper for Node.js

BACKGROUND: To cope with the ever-increasing amount of sequence data generated in the field of genomics, the demand for efficient and fast database searches that drive functional and structural annotation in both large- and small-scale genome projects is on the rise. The tools of the BLAST+ suite ar...

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Detalles Bibliográficos
Autores principales: Page, Martin, MacLean, Dan, Schudoma, Christian
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4769840/
https://www.ncbi.nlm.nih.gov/pubmed/26922376
http://dx.doi.org/10.1186/s13104-016-1938-1
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author Page, Martin
MacLean, Dan
Schudoma, Christian
author_facet Page, Martin
MacLean, Dan
Schudoma, Christian
author_sort Page, Martin
collection PubMed
description BACKGROUND: To cope with the ever-increasing amount of sequence data generated in the field of genomics, the demand for efficient and fast database searches that drive functional and structural annotation in both large- and small-scale genome projects is on the rise. The tools of the BLAST+ suite are the most widely employed bioinformatic method for these database searches. Recent trends in bioinformatics application development show an increasing number of JavaScript apps that are based on modern frameworks such as Node.js. Until now, there is no way of using database searches with the BLAST+ suite from a Node.js codebase. RESULTS: We developed blastjs, a Node.js library that wraps the search tools of the BLAST+ suite and thus allows to easily add significant functionality to any Node.js-based application. CONCLUSION: blastjs is a library that allows the incorporation of BLAST+ functionality into bioinformatics applications based on JavaScript and Node.js. The library was designed to be as user-friendly as possible and therefore requires only a minimal amount of code in the client application. The library is freely available under the MIT license at https://github.com/teammaclean/blastjs.
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spelling pubmed-47698402016-02-29 blastjs: a BLAST+ wrapper for Node.js Page, Martin MacLean, Dan Schudoma, Christian BMC Res Notes Technical Note BACKGROUND: To cope with the ever-increasing amount of sequence data generated in the field of genomics, the demand for efficient and fast database searches that drive functional and structural annotation in both large- and small-scale genome projects is on the rise. The tools of the BLAST+ suite are the most widely employed bioinformatic method for these database searches. Recent trends in bioinformatics application development show an increasing number of JavaScript apps that are based on modern frameworks such as Node.js. Until now, there is no way of using database searches with the BLAST+ suite from a Node.js codebase. RESULTS: We developed blastjs, a Node.js library that wraps the search tools of the BLAST+ suite and thus allows to easily add significant functionality to any Node.js-based application. CONCLUSION: blastjs is a library that allows the incorporation of BLAST+ functionality into bioinformatics applications based on JavaScript and Node.js. The library was designed to be as user-friendly as possible and therefore requires only a minimal amount of code in the client application. The library is freely available under the MIT license at https://github.com/teammaclean/blastjs. BioMed Central 2016-02-27 /pmc/articles/PMC4769840/ /pubmed/26922376 http://dx.doi.org/10.1186/s13104-016-1938-1 Text en © Page et al. 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Technical Note
Page, Martin
MacLean, Dan
Schudoma, Christian
blastjs: a BLAST+ wrapper for Node.js
title blastjs: a BLAST+ wrapper for Node.js
title_full blastjs: a BLAST+ wrapper for Node.js
title_fullStr blastjs: a BLAST+ wrapper for Node.js
title_full_unstemmed blastjs: a BLAST+ wrapper for Node.js
title_short blastjs: a BLAST+ wrapper for Node.js
title_sort blastjs: a blast+ wrapper for node.js
topic Technical Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4769840/
https://www.ncbi.nlm.nih.gov/pubmed/26922376
http://dx.doi.org/10.1186/s13104-016-1938-1
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