VarMap: a web tool for mapping genomic coordinates to protein sequence and structure and retrieving protein structural annotations

MOTIVATION: Understanding the protein structural context and patterning on proteins of genomic variants can help to separate benign from pathogenic variants and reveal molecular consequences. However, mapping genomic coordinates to protein structures is non-trivial, complicated by alternative splici...

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Detalles Bibliográficos
Autores principales: Stephenson, James D, Laskowski, Roman A, Nightingale, Andrew, Hurles, Matthew E, Thornton, Janet M
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2019
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6853667/
https://www.ncbi.nlm.nih.gov/pubmed/31192369
http://dx.doi.org/10.1093/bioinformatics/btz482
Descripción
Sumario:MOTIVATION: Understanding the protein structural context and patterning on proteins of genomic variants can help to separate benign from pathogenic variants and reveal molecular consequences. However, mapping genomic coordinates to protein structures is non-trivial, complicated by alternative splicing and transcript evidence. RESULTS: Here we present VarMap, a web tool for mapping a list of chromosome coordinates to canonical UniProt sequences and associated protein 3D structures, including validation checks, and annotating them with structural information. AVAILABILITY AND IMPLEMENTATION: https://www.ebi.ac.uk/thornton-srv/databases/VarMap. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

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