Dataset Information

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

ABSTRACT:

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.

SUBMITTER: Stephenson JD

PROVIDER: S-EPMC6853667 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

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Publications

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

Stephenson James D JD Laskowski Roman A RA Nightingale Andrew A Hurles Matthew E ME Thornton Janet M JM

Bioinformatics (Oxford, England) 20191101 22

<h4>Motivation</h4>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.<h4>Results</h4>Here we present VarMap, a web tool for mapping a list of chromosome coordinates to canonical UniProt sequences and associated protein 3D structures, i ...[more]

PMID: 31192369

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Project description:BackgroundAn individual's genetics play a role in how RNA transcripts are generated from DNA and consequently in their translation into protein. Transcriptional and translational profiling of patients furnishes the information that a specific marker is present; however, it fails to provide evidence whether the marker correlates with response to a therapeutic agent. A comparative analysis of the frequency of genetic variants, such as single nucleotide polymorphisms (SNPs), in diseased and general populations can identify pathogenic variants in individual patients. This is in part because SNPs have considerable effects on protein function and gene expression when they occur in coding regions and regulatory sequences, respectively. Therefore, a tool that can help users to obtain the allele frequency for a corresponding transcript is the need of the day. Several annotation tools such as SNPnexus and VariED are publicly available; however, none of them can use transcript IDs as input and provide the corresponding genomic positions of variants.ResultsIn this study, we developed an R package, called transcript annotation tool (TransAT), that provides (i) SNP ID and genomic position for a user-provided transcript ID from patients, and (ii) allele frequencies for the SNPs from publicly available global populations. All data elements are extracted, collected, and displayed in an easily downloadable format in two simple command lines. TransAT is available on Windows/Linux/MacOS and is operative for R version 4.0.4 or later. It is available at https://github.com/ShihChingYu/TransAT and can be downloaded and installed using devtools::install_github("ShihChingYu/TransAT", force=T) on the R execution page. Thereafter, all functions can be executed by loading the package into R with library(TransAT).ConclusionsTransAT is a novel tool that seamlessly provides genetic annotations for queried transcripts. Such easily obtainable information would be greatly advantageous for physicians, assisting them to make individualized decisions about specific drug treatments. Moreover, allele frequencies from user-chosen global ethnic populations will highlight the importance of ethnicity and its effect on patient pathogenicity.

Dataset Information

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

Motivation

Results

Availability and implementation

Supplementary information

Publications

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

Similar Datasets

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