Evidence map›Paper›PMID 37753479›Full record

ArticleGigaByte (Hong Kong, China)2023

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

Eamon Winden, Alejandro Vasquez-Echeverri, Susana Calle-Castañeda, Yumin Lian, Juan Pablo Hernandez Ortiz, David C Schwartz

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in GigaByte (Hong Kong, China), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

6 authors.

Eamon WindenLaboratory of Genetics, Department of Chemistry, Laboratory for Molecular and Computational Genomics, University of Wisconsin-Madison, Madison, WI 53705, USA.ORCID https://orcid.org/0000-0002-3415-0264
Alejandro Vasquez-EcheverriDepartment of Biophysics, Department of Genetics, Department of Chemistry, Laboratory for Molecular and Computational Genomics, University of Wisconsin-Madison, Madison, WI 53705, USA.ORCID https://orcid.org/0000-0001-6894-2617
Susana Calle-CastañedaLaboratory of Genetics, Department of Chemistry, Laboratory for Molecular and Computational Genomics, University of Wisconsin-Madison, Madison, WI 53705, USA.ORCID https://orcid.org/0009-0003-4986-6358
Yumin LianLaboratory of Genetics, Department of Chemistry, Laboratory for Molecular and Computational Genomics, University of Wisconsin-Madison, Madison, WI 53705, USA.ORCID https://orcid.org/0009-0002-3663-3398
Juan Pablo Hernandez OrtizDepartamento de Materiales y Nanotecnología, Universidad Nacional de Colombia - Medellín, Medellín, 050034, Colombia.ORCID https://orcid.org/0000-0003-0404-9947
David C SchwartzLaboratory of Genetics, Department of Chemistry, Laboratory for Molecular and Computational Genomics, University of Wisconsin-Madison, Madison, WI 53705, USA.ORCID https://orcid.org/0000-0002-4726-3241

Funding

Institutional Training in the Genomic SciencesT32HG002760 · NHGRI · UNIVERSITY OF WISCONSIN-MADISON · PI Qiongshi Lu · 2003 to 2026
$17.7M
PREDOCTORAL TRAINING PROGRAM IN GENETICST32GM007133 · NIGMS · UNIVERSITY OF WISCONSIN-MADISON · PI PERNA, NICOLE T · 1985 to 2023
$16.5M
GenSyn: A Cycle for Serial Assembly of Very Large DNA MoleculesR21HG012281 · NHGRI · UNIVERSITY OF WISCONSIN-MADISON · PI SCHWARTZ, DAVID C. · 2022 to 2024
$607k
NHGRI NIH HHS R21 HG012281NHGRI NIH HHS T32 HG002760NIGMS NIH HHS T32 GM007133
6 · The paper itself

Abstract

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.

Identifiers

PMID37753479
PMCPMC10518450

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.