Document Type

Journal Article

Publication Date

2014

Journal

BIoinformatics

Abstract

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 data sets.

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: BioClojure is distributed under the Lesser GPL (LGPL) and the source code is freely available from GitHub (https://github.com/s312569/clj-biosequence).

Contact: jason.mulvenna@qimr.edu.au

Comments

Reproduced with permission of Oxford University Press, Bioinformatics.

Creative Commons License

Creative Commons License
This work is licensed under a Creative Commons Attribution 3.0 License.

Open Access

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