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Bioinformatics. 2018 Jun 1;34(11):1949-1950. doi: 10.1093/bioinformatics/bty047.

G2S: a web-service for annotating genomic variants on 3D protein structures.

Author information

1
Department of Electrical Engineering & Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
2
Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
3
Department of Epidemiology-Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.

Abstract

Motivation:

Accurately mapping and annotating genomic locations on 3D protein structures is a key step in structure-based analysis of genomic variants detected by recent large-scale sequencing efforts. There are several mapping resources currently available, but none of them provides a web API (Application Programming Interface) that supports programmatic access.

Results:

We present G2S, a real-time web API that provides automated mapping of genomic variants on 3D protein structures. G2S can align genomic locations of variants, protein locations, or protein sequences to protein structures and retrieve the mapped residues from structures. G2S API uses REST-inspired design and it can be used by various clients such as web browsers, command terminals, programming languages and other bioinformatics tools for bringing 3D structures into genomic variant analysis.

Availability and implementation:

The webserver and source codes are freely available at https://g2s.genomenexus.org.

Contact:

g2s@genomenexus.org.

Supplementary information:

Supplementary data are available at Bioinformatics online.

PMID:
29385402
PMCID:
PMC5972642
DOI:
10.1093/bioinformatics/bty047
[Indexed for MEDLINE]
Free PMC Article

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