BioStructMap: a Python tool for integration of protein structure and sequence-based features | Zendy

Andrew J. Guy | Zendy; Vashti Irani | Zendy; Jack S. Richards | Zendy; Paul A. Ramsland | Zendy

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BioStructMap: a Python tool for integration of protein structure and sequence-based features

Author(s) -

Andrew J. Guy,

Vashti Irani,

Jack S. Richards,

Paul A. Ramsland

Publication year - 2018

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/bty474

Subject(s) - python (programming language) , mit license , computer science , sliding window protocol , software , extensibility , programming language , sequence alignment , data structure , computational biology , data mining , biology , window (computing) , operating system , peptide sequence , gene , genetics

A sliding window analysis over a protein or genomic sequence is commonly performed, and we present a Python tool, BioStructMap, that extends this concept to three-dimensional (3D) space, allowing the application of a 3D sliding window analysis over a protein structure. BioStructMap is easily extensible, allowing the user to apply custom functions to spatially aggregated data. BioStructMap also allows mapping of underlying genomic sequences to protein structures, allowing the user to perform genetic-based analysis over spatially linked codons-this has applications when selection pressures arise at the level of protein structure.

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