STRprofiler: efficient comparisons of short tandem repeat profiles for biomedical model authentication.

Autor:	Andrews JM; Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, United States., Lloyd MW; The Jackson Laboratory, Bar Harbor, ME 04609, United States., Neuhauser SB; The Jackson Laboratory, Bar Harbor, ME 04609, United States., Bundy M; The Jackson Laboratory, Sacramento, CA 95838, United States., Jocoy EL; The Jackson Laboratory, Sacramento, CA 95838, United States., Airhart SD; The Jackson Laboratory, Bar Harbor, ME 04609, United States., Bult CJ; The Jackson Laboratory, Bar Harbor, ME 04609, United States., Evrard YA; Leidos Biomedical Research, Inc, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, United States., Chuang JH; The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, United States., Baker S; Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, United States.
Jazyk:	angličtina
Zdroj:	Bioinformatics (Oxford, England) [Bioinformatics] 2024 Nov 28; Vol. 40 (12).
DOI:	10.1093/bioinformatics/btae713
Abstrakt:	Summary: Short tandem repeat (STR) profiling is commonly performed for authentication of biomedical models of human origin, yet no tools exist to easily compare sets of STR profiles to each other or an existing database in a high-throughput manner. Here, we present STRprofiler, a Python package, command line tool, and Shiny application providing methods for STR profile comparison and cross-contamination detection. STRprofiler can be run with custom databases or used to query against the Cellosaurus cell line database. Availability and Implementation: STRprofiler is freely available as a Python package with a rich CLI from PyPI https://pypi.org/project/strprofiler/ with source code available under the MIT license on GitHub https://github.com/j-andrews7/strprofiler and at https://zenodo.org/records/10989034. A web server hosting an example STRprofiler Shiny application backed by a database with data from the National Cancer Institute-funded PDXNet consortium and The Jackson Laboratory PDX program is available at https://sj-bakerlab.shinyapps.io/strprofiler/. Full documentation is available at https://strprofiler.readthedocs.io/en/latest/. (© The Author(s) 2024. Published by Oxford University Press.)
Databáze:	MEDLINE
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