Dataset Information

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

ABSTRACT:

Summary

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.

Availability and implementation

The Python BioStructMap package is available at https://github.com/andrewguy/biostructmap and released under the MIT License. An online server implementing standard functionality is available at https://biostructmap.burnet.edu.au.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Guy AJ

PROVIDER: S-EPMC6223362 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature

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Publications

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

Guy Andrew J AJ Irani Vashti V Richards Jack S JS Ramsland Paul A PA

Bioinformatics (Oxford, England) 20181101 22

<h4>Summary</h4>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 ...[more]

PMID: 29931276

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Dataset Information

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

Summary

Availability and implementation

Supplementary information

Publications

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

Similar Datasets

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