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bioSyntax: Syntax Highlighting For Computational Biology

View ORCID ProfileArtem Babaian, Anicet Ebou, Alyssa Fegen, Ho Yin (Jeffrey) Kam, German E. Novakovsky, Jasper Wong
doi: https://doi.org/10.1101/235820
Artem Babaian
1Terry Fox Laboratory, BC Cancer, Vancouver, BC, Canada. []
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  • For correspondence: artem@rRNA.ca artem@rRNA.ca
Anicet Ebou
2Departement de Formation et de Recherches Agriculture et Ressources Animales, Institut National Polytechnique Felix Houphouet-Boigny, Yamoussoukro, Côte d’Ivoire. []
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  • For correspondence: anicet.ebou@gmail.com
Alyssa Fegen
3Faculty of Science, University of British Columbia, Vancouver, BC, Canada []
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  • For correspondence: alyssafegen@alumni.ubc.ca
Ho Yin (Jeffrey) Kam
4Faculty of Mathematics, University of Waterloo, Waterloo, ON, Canada. []
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  • For correspondence: hykam@edu.uwaterloo.ca
German E. Novakovsky
5Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada. []
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  • For correspondence: gnovakovsky@cmmt.ubc.ca
Jasper Wong
6Genome Science and Technology, University of British Columbia, Vancouver, BC, Canada. []
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  • For correspondence: jawong@bcgsc.ca
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Abstract

Computational biology requires the reading and comprehension of biological data files. Plain-text formats such as SAM, VCF, GTF, PDB and FASTA, often contain critical information that is obfuscated by the complexity of the data structures. bioSyntax (http://bioSyntax.org) is a freely available suite of syntax highlighting packages for vim, gedit, Sublime, and less, which aids computational scientists to parse and work with their data more efficiently.

  • List of Abbreviations

    GTF
    : Gene Transfer Format
    IUPAC
    : International Union of Pure and Applied Chemistry
    PDB
    : Protein Database Format
    SAM
    : Sequence Alignment Map
    VCF
    : Variant Call Format
  • Copyright 
    The copyright holder has placed this preprint in the Public Domain. It is no longer restricted by copyright. Anyone can legally share, reuse, remix, or adapt this material for any purpose without crediting the original authors.
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    Posted December 20, 2017.
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    bioSyntax: Syntax Highlighting For Computational Biology
    Artem Babaian, Anicet Ebou, Alyssa Fegen, Ho Yin (Jeffrey) Kam, German E. Novakovsky, Jasper Wong
    bioRxiv 235820; doi: https://doi.org/10.1101/235820
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    bioSyntax: Syntax Highlighting For Computational Biology
    Artem Babaian, Anicet Ebou, Alyssa Fegen, Ho Yin (Jeffrey) Kam, German E. Novakovsky, Jasper Wong
    bioRxiv 235820; doi: https://doi.org/10.1101/235820

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