3Dmapper : a command line tool for BioBank-scale mapping of variants to protein structures
Ruiz-Serra, Victoria (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras)
Valentini, Samuel (University of Trento)
Madroñero, Sergi (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras)
Valencia, Alfonso (Institució Catalana de Recerca i Estudis Avançats)
Porta-Pardo, Eduard (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras)

Date:	2024
Abstract:	Motivation: 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. Results: To address this issue, we introduce 3Dmapper, a stand-alone 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.
Grants:	"la Caixa" Foundation LCF/BQ/PI18/11630003 Agencia Estatal de Investigación PID2019-107043RA-I00
Rights:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Language:	Anglès
Document:	Article ; recerca ; Versió publicada
Subject:	Biological Specimen Banks ; Genomics ; Proteins ; Software
Published in:	Bioinformatics, Vol. 40 Núm. 4 (january 2024) , p. btae171, ISSN 1367-4811

DOI: 10.1093/bioinformatics/btae171
PMID: 38565273

5 p, 2.1 MB

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Research literature > UAB research groups literature > Research Centres and Groups (research output) > Health sciences and biosciences > Institut d'Investigació en Ciencies de la Salut Germans Trias i Pujol (IGTP) > Josep Carreras Leukaemia Research Institute
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