Bioclojure: a functional library for the manipulation of biological sequences

Plieskatt, Jordan, Rinaldi, Gabriel, Brindley, Paul J., Jia, Xinying, Potriquet, Jeremy, Bethony, Jeffrey and Mulvenna, Jason (2014) Bioclojure: a functional library for the manipulation of biological sequences. Bioinformatics, 30 17: 2537-2539. doi:10.1093/bioinformatics/btu311


Author Plieskatt, Jordan
Rinaldi, Gabriel
Brindley, Paul J.
Jia, Xinying
Potriquet, Jeremy
Bethony, Jeffrey
Mulvenna, Jason
Title Bioclojure: a functional library for the manipulation of biological sequences
Journal name Bioinformatics   Check publisher's open access policy
ISSN 1460-2059
1367-4803
1367-4811
Publication date 2014-09-01
Year available 2014
Sub-type Article (original research)
DOI 10.1093/bioinformatics/btu311
Open Access Status
Volume 30
Issue 17
Start page 2537
End page 2539
Total pages 3
Place of publication Oxford, United Kingdom
Publisher Oxford University Press
Collection year 2015
Language eng
Formatted 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 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.
Keyword Bioclojure
Biological sequence data
Q-Index Code CX
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Non HERDC
School of Biomedical Sciences Publications
 
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