EDIR: exome database of interspersed repeats

Author:

Vo Ngoc Laura D T1,Osei Randy1,Dohr Katrin2,Olsen Catharina134,Seneca Sara1,Gheldof Alexander1ORCID

Affiliation:

1. Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Clinical Sciences, Research Group Reproduction and Genetics, Centre for Medical Genetics , Brussels 1090, Belgium

2. Department of Paediatrics and Adolescent Medicine, Research Unit of Analytical Mass Spectrometry, Cell Biology and Biochemistry of Inborn Errors of Metabolism , Graz 8010, Austria

3. Brussels Interuniversity Genomics High Throughput Core (BRIGHTcore), VUB-ULB , Brussels 1090, Belgium

4. Interuniversity Institute of Bioinformatics in Brussels (IB)2, VUB-ULB , Brussels 1050, Belgium

Abstract

Abstract 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.

Funder

Wetenschappelijk Fonds Willy Gepts

Universitair Ziekenhuis Brussel

Publisher

Oxford University Press (OUP)

Subject

Computational Mathematics,Computational Theory and Mathematics,Computer Science Applications,Molecular Biology,Biochemistry,Statistics and Probability

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