TY - JOUR
T1 - Bioclojure
T2 - A functional library for the manipulation of biological sequences
AU - Plieskatt, Jordan
AU - Rinaldi, Gabriel
AU - Brindley, Paul J.
AU - Jia, Xinying
AU - Potriquet, Jeremy
AU - Bethony, Jeffrey
AU - Mulvenna, Jason
N1 - © The Author 2014. Published by Oxford University Press.
PY - 2014/9/1
Y1 - 2014/9/1
N2 - 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.
AB - 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.
KW - High-Throughput Nucleotide Sequencing/methods
KW - Programming Languages
KW - Sequence Analysis, Protein/methods
KW - Software
UR - http://www.scopus.com/inward/record.url?scp=84907031428&partnerID=8YFLogxK
U2 - 10.1093/bioinformatics/btu311
DO - 10.1093/bioinformatics/btu311
M3 - Article
C2 - 24794932
AN - SCOPUS:84907031428
SN - 1367-4803
VL - 30
SP - 2537
EP - 2539
JO - Bioinformatics
JF - Bioinformatics
IS - 17
ER -