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Bioclojure: a functional library for the manipulation of biological sequences
Jordan Plieskatt1, Gabriel Rinaldi1, Paul J Brindley1
1Department of Microbiology, Immunology and Tropical Medicine, Research Center for Neglected Diseases of Poverty, School of Medicine and Health Sciences, George Washington University, Washington, DC, 20052, USA, QIMR Berghofer Medical Research Institute, Infectious Disease and Cancer and The University of Queensland, School of Biomedical Sciences, Brisbane, Queensland, 4072, Australia Department of Microbiology, Immunology and Tropical Medicine, Research Center for Neglected Diseases of Poverty, School of Medicine and Health Sciences, George Washington University, Washington, DC, 20052, USA, QIMR Berghofer Medical Research Institute, Infectious Disease and Cancer and The University of Queensland, School of Biomedical Sciences, Brisbane, Queensland, 4072, Australia.
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).
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