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3Dmapper: A Command Line Tool For BioBank-scale Mapping Of Variants To Protein Structures
Open accessPreprint — published as 10.1093/bioinformatics/btae171 · Paper page
Abstract
The interpretation of genomic data is crucial to understand the molecular mechanisms of biological processes. Protein structures play a vital role in facilitating this interpretation by providing functional context to genetic coding variants. However, mapping genes to proteins is a tedious and error-prone task due to inconsistencies in data formats. Over the past two decades, numerous tools and databases have been developed to automatically map annotated positions and variants to protein structures. However, most of these tools are web-based and not well-suited for large-scale genomic data analysis. To address this issue, we introduce 3Dmapper, a standalone command-line tool developed in Python and R. It systematically maps annotated protein positions and variants to protein structures, providing a solution that is both efficient and reliable. 3Dmapper is freely available on GitHub at https://github.com/vicruiser/3Dmapper .
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Metadata
- Authors
- Ruiz-Serra, V., Valentini, S., Madroñero, S., Valencia, A., & Porta-Pardo, E.
- Affiliations
- University of Trento (IT)
- Josep Carreras Leukaemia Research Institute (ES)
- Institució Catalana de Recerca i Estudis Avançats (ES)
- Venue
- Bioinformatics
- Publisher
- openRxiv
- Published
- 2023-09-05
- Volume
- 40
- Issue
- 4
- ISSN
- 1367-4803 (ISSN-L)
- PMC
- PMC11018535
- OpenAlex
- W4393407391
- Cited by
- 0
- References
- 1
- FWCI
- 0.00
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- Bioinformatics (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- UPCommons institutional repository (Universitat Politècnica de Catalunya) (submittedVersion, cc-by-nc-nd)
- Dipòsit Digital de Documents de la UAB (Universitat Autònoma de Barcelona) (submittedVersion, cc-by)
- Funders
- Institució Catalana de Recerca i Estudis Avançats
- Barcelona Supercomputing Center
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Keywords
- protein structure, genetic variants, genomic data interpretation, command-line tool, genome annotation
- MeSH terms
- Proteins, Software, Biological Specimen Banks, Genomics
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