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Bioclojure: a functional library for the manipulation of biological sequences

Motivation: BioClojure is an open-source library for the manipulation of biological sequence data written in the language Clojure. BioClojure aims to provide a functional framework for the processing of biological sequence data that provides simple mechanisms for concurrency and lazy evaluation of l...

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Detalles Bibliográficos
Autores principales: Plieskatt, Jordan, Rinaldi, Gabriel, Brindley, Paul J., Jia, Xinying, Potriquet, Jeremy, Bethony, Jeffrey, Mulvenna, Jason
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4147884/
https://www.ncbi.nlm.nih.gov/pubmed/24794932
http://dx.doi.org/10.1093/bioinformatics/btu311
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author Plieskatt, Jordan
Rinaldi, Gabriel
Brindley, Paul J.
Jia, Xinying
Potriquet, Jeremy
Bethony, Jeffrey
Mulvenna, Jason
author_facet Plieskatt, Jordan
Rinaldi, Gabriel
Brindley, Paul J.
Jia, Xinying
Potriquet, Jeremy
Bethony, Jeffrey
Mulvenna, Jason
author_sort Plieskatt, Jordan
collection PubMed
description Motivation: BioClojure is an open-source library for the manipulation of biological sequence data written in the language Clojure. BioClojure aims to provide a functional framework for the processing of biological sequence data that provides simple mechanisms for concurrency and lazy evaluation of large datasets. Results: BioClojure provides parsers and accessors for a range of biological sequence formats, including UniProtXML, Genbank XML, FASTA and FASTQ. In addition, it provides wrappers for key analysis programs, including BLAST, SignalP, TMHMM and InterProScan, and parsers for analyzing their output. All interfaces leverage Clojure’s functional style and emphasize laziness and composability, so that BioClojure, and user-defined, functions can be chained into simple pipelines that are thread-safe and seamlessly integrate lazy evaluation. Availability and implementation: BioClojure is distributed under the Lesser GPL, and the source code is freely available from GitHub (https://github.com/s312569/clj-biosequence). Contact: jason.mulvenna@qimrberghofer.edu.au or jason.mulvenna@qimr.edu.au
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spelling pubmed-41478842014-09-02 Bioclojure: a functional library for the manipulation of biological sequences Plieskatt, Jordan Rinaldi, Gabriel Brindley, Paul J. Jia, Xinying Potriquet, Jeremy Bethony, Jeffrey Mulvenna, Jason Bioinformatics Applications Notes Motivation: BioClojure is an open-source library for the manipulation of biological sequence data written in the language Clojure. BioClojure aims to provide a functional framework for the processing of biological sequence data that provides simple mechanisms for concurrency and lazy evaluation of large datasets. Results: BioClojure provides parsers and accessors for a range of biological sequence formats, including UniProtXML, Genbank XML, FASTA and FASTQ. In addition, it provides wrappers for key analysis programs, including BLAST, SignalP, TMHMM and InterProScan, and parsers for analyzing their output. All interfaces leverage Clojure’s functional style and emphasize laziness and composability, so that BioClojure, and user-defined, functions can be chained into simple pipelines that are thread-safe and seamlessly integrate lazy evaluation. Availability and implementation: BioClojure is distributed under the Lesser GPL, and the source code is freely available from GitHub (https://github.com/s312569/clj-biosequence). Contact: jason.mulvenna@qimrberghofer.edu.au or jason.mulvenna@qimr.edu.au Oxford University Press 2014-09-01 2014-05-02 /pmc/articles/PMC4147884/ /pubmed/24794932 http://dx.doi.org/10.1093/bioinformatics/btu311 Text en © The Author 2014. Published by Oxford University Press. http://creativecommons.org/licenses/by/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Notes
Plieskatt, Jordan
Rinaldi, Gabriel
Brindley, Paul J.
Jia, Xinying
Potriquet, Jeremy
Bethony, Jeffrey
Mulvenna, Jason
Bioclojure: a functional library for the manipulation of biological sequences
title Bioclojure: a functional library for the manipulation of biological sequences
title_full Bioclojure: a functional library for the manipulation of biological sequences
title_fullStr Bioclojure: a functional library for the manipulation of biological sequences
title_full_unstemmed Bioclojure: a functional library for the manipulation of biological sequences
title_short Bioclojure: a functional library for the manipulation of biological sequences
title_sort bioclojure: a functional library for the manipulation of biological sequences
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4147884/
https://www.ncbi.nlm.nih.gov/pubmed/24794932
http://dx.doi.org/10.1093/bioinformatics/btu311
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