EDIR: exome database of interspersed repeats.
Journal
Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944
Informations de publication
Date de publication:
01 01 2023
01 01 2023
Historique:
received:
03
02
2022
revised:
12
11
2022
accepted:
30
11
2022
pubmed:
2
12
2022
medline:
4
1
2023
entrez:
1
12
2022
Statut:
ppublish
Résumé
Intragenic exonic deletions are known to contribute to genetic diseases and are often flanked by regions of homology. In order to get a more clear view of these interspersed repeats encompassing a coding sequence, we have developed EDIR (Exome Database of Interspersed Repeats) which contains the positions of these structures within the human exome. EDIR has been calculated by an inductive strategy, rather than by a brute force approach and can be queried through an R/Bioconductor package or a web interface allowing the per-gene rapid extraction of homology-flanked sequences throughout the exome. The code used to compile EDIR can be found at https://github.com/lauravongoc/EDIR. The full dataset of EDIR can be queried via an Rshiny application at http://193.70.34.71:3857/edir/. The R package for querying EDIR is called 'EDIRquery' and is available on Bioconductor. The full EDIR dataset can be downloaded from https://osf.io/m3gvx/ or http://193.70.34.71/EDIR.tar.gz. Supplementary data are available at Bioinformatics online.
Identifiants
pubmed: 36453866
pii: 6858440
doi: 10.1093/bioinformatics/btac771
pmc: PMC9805566
pii:
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : Wetenschappelijk Fonds Willy Gepts
Organisme : Universitair Ziekenhuis Brussel
Informations de copyright
© The Author(s) 2022. Published by Oxford University Press.
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