Bioclojure: a functional library for the manipulation of biological sequences.
Bioclojure: a functional library for the manipulation of biological sequences.
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Bioclojure：用于操作生物序列的功能库。
DOI：
10.1093/bioinformatics/btu311
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发表时间：
2014
期刊：
影响因子：
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通讯作者：
Mulvenna,Jason
中科院分区：
文献类型：
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作者：
Plieskatt,Jordan;Rinaldi,Gabriel;Brindley,PaulJ;Jia,Xinying;Potriquet,Jeremy;Bethony,Jeffrey;Mulvenna,Jason
BioClojure是一个开源库，用于操作用Clojure语言编写的生物序列数据。BioClojure旨在为生物序列数据的处理提供一个功能框架，为大型datasets.Results的并发和惰性评估提供简单的机制：BioClojure提供了一系列生物序列格式的解析器和访问器，包括UniProtXML，Genbank XML，FASTA和FASTQ。此外，它还提供了关键分析程序（包括BLAST、SignalP、TMHMM和InterProScan）的包装器以及用于分析其输出的解析器。所有接口都利用了Clojure的函数式风格，并强调了惰性和可组合性，因此BioClojure和用户定义的函数可以链接到简单的管道中，这些管道是线程安全的，并无缝集成了惰性评估。可用性和实现：BioClojure在Lesser GPL下分发，源代码可以从GitHub（https：//github.com/s312569/clj-biosequence）免费获得。联系方式：jason. mulvenna @ qimrberghofer.edu.au或jason. qimr.edu.au
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