title: Bioclojure: a functional library for the manipulation of biological sequences.
abstract: BACKGROUND
  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.
  
  
  METHODS
  BioClojure is distributed under the Lesser GPL, and the source code is freely available from GitHub (https://github.com/s312569/clj-biosequence).
authors.affiliation: 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 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.
authors.forename: Jordan
authors.initials: J
authors.lastname: Plieskatt
authors.affiliation: 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 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.
authors.forename: Gabriel
authors.initials: G
authors.lastname: Rinaldi
authors.affiliation: 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 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.
authors.forename: Paul J
authors.initials: PJ
authors.lastname: Brindley
authors.affiliation: 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.
authors.forename: Xinying
authors.initials: X
authors.lastname: Jia
authors.affiliation: 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.
authors.forename: Jeremy
authors.initials: J
authors.lastname: Potriquet
authors.affiliation: 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.
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Bethony
authors.affiliation: 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 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.
authors.forename: Jason
authors.initials: J
authors.lastname: Mulvenna
mesh_terms: D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D011381:Programming Languages; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software