Cargando…

A database of restriction maps to expand the utility of bacterial artificial chromosomes

While Bacterial Artificial Chromosomes libraries were once a key resource for the genomic community, they have been obviated, for sequencing purposes, by long-read technologies. Such libraries may now serve as a valuable resource for manipulating and assembling large genomic constructs. To enhance a...

Descripción completa

Detalles Bibliográficos
Autores principales: Winden, Eamon, Vasquez-Echeverri, Alejandro, Calle-Castañeda, Susana, Lian, Yumin, Hernandez Ortiz, Juan Pablo, Schwartz, David C.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: GigaScience Press 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10518450/
https://www.ncbi.nlm.nih.gov/pubmed/37753479
http://dx.doi.org/10.46471/gigabyte.93
_version_ 1785109516524716032
author Winden, Eamon
Vasquez-Echeverri, Alejandro
Calle-Castañeda, Susana
Lian, Yumin
Hernandez Ortiz, Juan Pablo
Schwartz, David C.
author_facet Winden, Eamon
Vasquez-Echeverri, Alejandro
Calle-Castañeda, Susana
Lian, Yumin
Hernandez Ortiz, Juan Pablo
Schwartz, David C.
author_sort Winden, Eamon
collection PubMed
description While Bacterial Artificial Chromosomes libraries were once a key resource for the genomic community, they have been obviated, for sequencing purposes, by long-read technologies. Such libraries may now serve as a valuable resource for manipulating and assembling large genomic constructs. To enhance accessibility and comparison, we have developed a BAC restriction map database. Using information from the National Center for Biotechnology Information’s cloneDB FTP site, we constructed a database containing the restriction maps for both uniquely placed and insert-sequenced BACs from 11 libraries covering the recognition sequences of the available restriction enzymes. Along with the database, we generated a set of Python functions to reconstruct the database and more easily access the information within. This data is valuable for researchers simply using BACs, as well as those working with larger sections of the genome in terms of synthetic genes, large-scale editing, and mapping.
format Online
Article
Text
id pubmed-10518450
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher GigaScience Press
record_format MEDLINE/PubMed
spelling pubmed-105184502023-09-26 A database of restriction maps to expand the utility of bacterial artificial chromosomes Winden, Eamon Vasquez-Echeverri, Alejandro Calle-Castañeda, Susana Lian, Yumin Hernandez Ortiz, Juan Pablo Schwartz, David C. GigaByte Data Release While Bacterial Artificial Chromosomes libraries were once a key resource for the genomic community, they have been obviated, for sequencing purposes, by long-read technologies. Such libraries may now serve as a valuable resource for manipulating and assembling large genomic constructs. To enhance accessibility and comparison, we have developed a BAC restriction map database. Using information from the National Center for Biotechnology Information’s cloneDB FTP site, we constructed a database containing the restriction maps for both uniquely placed and insert-sequenced BACs from 11 libraries covering the recognition sequences of the available restriction enzymes. Along with the database, we generated a set of Python functions to reconstruct the database and more easily access the information within. This data is valuable for researchers simply using BACs, as well as those working with larger sections of the genome in terms of synthetic genes, large-scale editing, and mapping. GigaScience Press 2023-09-20 /pmc/articles/PMC10518450/ /pubmed/37753479 http://dx.doi.org/10.46471/gigabyte.93 Text en © The Author(s) 2023. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Data Release
Winden, Eamon
Vasquez-Echeverri, Alejandro
Calle-Castañeda, Susana
Lian, Yumin
Hernandez Ortiz, Juan Pablo
Schwartz, David C.
A database of restriction maps to expand the utility of bacterial artificial chromosomes
title A database of restriction maps to expand the utility of bacterial artificial chromosomes
title_full A database of restriction maps to expand the utility of bacterial artificial chromosomes
title_fullStr A database of restriction maps to expand the utility of bacterial artificial chromosomes
title_full_unstemmed A database of restriction maps to expand the utility of bacterial artificial chromosomes
title_short A database of restriction maps to expand the utility of bacterial artificial chromosomes
title_sort database of restriction maps to expand the utility of bacterial artificial chromosomes
topic Data Release
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10518450/
https://www.ncbi.nlm.nih.gov/pubmed/37753479
http://dx.doi.org/10.46471/gigabyte.93
work_keys_str_mv AT windeneamon adatabaseofrestrictionmapstoexpandtheutilityofbacterialartificialchromosomes
AT vasquezecheverrialejandro adatabaseofrestrictionmapstoexpandtheutilityofbacterialartificialchromosomes
AT callecastanedasusana adatabaseofrestrictionmapstoexpandtheutilityofbacterialartificialchromosomes
AT lianyumin adatabaseofrestrictionmapstoexpandtheutilityofbacterialartificialchromosomes
AT hernandezortizjuanpablo adatabaseofrestrictionmapstoexpandtheutilityofbacterialartificialchromosomes
AT schwartzdavidc adatabaseofrestrictionmapstoexpandtheutilityofbacterialartificialchromosomes
AT windeneamon databaseofrestrictionmapstoexpandtheutilityofbacterialartificialchromosomes
AT vasquezecheverrialejandro databaseofrestrictionmapstoexpandtheutilityofbacterialartificialchromosomes
AT callecastanedasusana databaseofrestrictionmapstoexpandtheutilityofbacterialartificialchromosomes
AT lianyumin databaseofrestrictionmapstoexpandtheutilityofbacterialartificialchromosomes
AT hernandezortizjuanpablo databaseofrestrictionmapstoexpandtheutilityofbacterialartificialchromosomes
AT schwartzdavidc databaseofrestrictionmapstoexpandtheutilityofbacterialartificialchromosomes