EDIR: exome database of interspersed repeats
Related Experiment Video
Updated: Aug 19, 2025

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
Published on: April 4, 2018
Laura D T Vo Ngoc1, Randy Osei1, Katrin Dohr2
1Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Clinical Sciences, Research Group Reproduction and Genetics, Centre for Medical Genetics, Brussels 1090, Belgium.
Motivation:
Intragenic exonic deletions are known to contribute to genetic diseases and are often flanked by regions of homology.
Results:
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.
Availability And Implementation:
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 Information:
Supplementary data are available at Bioinformatics online.
Related Concept Videos
Exon Recombination
Exon shuffling follows “splice frame rules.” Each exon...
Non-LTR Retrotransposons
Genomic DNA in Eukaryotes
DNA Microarrays
Multi-species Conserved Sequences
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
RNA-seq
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...

