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
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author Stephenson, James D
Laskowski, Roman A
Nightingale, Andrew
Hurles, Matthew E
Thornton, Janet M
author_facet Stephenson, James D
Laskowski, Roman A
Nightingale, Andrew
Hurles, Matthew E
Thornton, Janet M
author_sort Stephenson, James D
collection PubMed
description 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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spelling pubmed-68536672019-11-19 VarMap: a web tool for mapping genomic coordinates to protein sequence and structure and retrieving protein structural annotations Stephenson, James D Laskowski, Roman A Nightingale, Andrew Hurles, Matthew E Thornton, Janet M Bioinformatics Applications Notes 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. Oxford University Press 2019-11-15 2019-06-13 /pmc/articles/PMC6853667/ /pubmed/31192369 http://dx.doi.org/10.1093/bioinformatics/btz482 Text en © The Author(s) 2019. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Notes
Stephenson, James D
Laskowski, Roman A
Nightingale, Andrew
Hurles, Matthew E
Thornton, Janet M
VarMap: a web tool for mapping genomic coordinates to protein sequence and structure and retrieving protein structural annotations
title VarMap: a web tool for mapping genomic coordinates to protein sequence and structure and retrieving protein structural annotations
title_full VarMap: a web tool for mapping genomic coordinates to protein sequence and structure and retrieving protein structural annotations
title_fullStr VarMap: a web tool for mapping genomic coordinates to protein sequence and structure and retrieving protein structural annotations
title_full_unstemmed VarMap: a web tool for mapping genomic coordinates to protein sequence and structure and retrieving protein structural annotations
title_short VarMap: a web tool for mapping genomic coordinates to protein sequence and structure and retrieving protein structural annotations
title_sort varmap: a web tool for mapping genomic coordinates to protein sequence and structure and retrieving protein structural annotations
topic Applications Notes
url 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
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