LOGIQA: a database dedicated to long-range genome interactions quality assessment.
BMC Genomics
; 17: 355, 2016 05 16.
Article
in En
| MEDLINE
| ID: mdl-27185059
ABSTRACT
BACKGROUND:
Proximity ligation-mediated methods are essential to study the impact of three-dimensional chromatin organization on gene programming. Albeit significant progress has been made in the development of computational tools that assess long-range chromatin interactions, next to nothing is known about the quality of the generated datasets.METHOD:
We have developed LOGIQA ( www.ngs-qc.org/logiqa ), a database hosting quality scores for long-range genome interaction assays, accessible through a user-friendly web-based environment.RESULTS:
Currently, LOGIQA harbors QC scores for >900 datasets, which provides a global view of their relative quality and reveals the impact of genome size, coverage and other technical aspects. LOGIQA provides a user-friendly dataset query panel and a genome viewer to assess local genome-interaction maps at different resolution and quality-assessment conditions.CONCLUSIONS:
LOGIQA is the first database hosting quality scores dedicated to long-range chromatin interaction assays, which in addition provides a platform for visualizing genome interactions made available by the scientific community.Key words
Full text:
1
Database:
MEDLINE
Main subject:
Software
/
Genome
/
Genomics
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Databases, Genetic
Language:
En
Year:
2016
Type:
Article