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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...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2014
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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 |
format | Online Article Text |
id | pubmed-4147884 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
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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