Charles, O. J. | bioRxiv Science

bioRxiv2021

WeightedLD: The Application of Sequence Weights to Linkage Disequilibrium

Sequence-weighting methods are commonly employed to account for biases in sequence datasets. We use a weighting scheme which considers the observed distinctiveness of sequences and apply it to calculations of linkage disequilibrium. Each sequence now contributes a weighted score to linkage disequilibrium measurements of pairwise loci. We demonstrate that this reduces the effect of uneven sampling, as underrepresented groups of sequences will each contribute more individually than redundant, similar sequences. AvailabilitySource code for a python and rust implementation are freely available at under an MIT license at github.com/ojcharles/WeightedLD. Contactr.goldstein@ucl.ac.uk or oscar.charles.18@ucl.ac.uk

genetics↗

bioRxiv2020

cmvdrg - An R package for Human Cytomegalovirus antiviral Drug Resistance Genotyping

The prevention and treatment of many herpesvirus associated diseases is based on the utilization of antiviral therapies, however therapeutic success is limited by the development of drug resistance. A comprehensive point of truth of resistance conferring mutations has been missing but would be important to aid the development of antiviral drugs and in management of infections. We therefore developed HerpesDRG, a drug resistance mutation database for all the known important genes and current treatment options, built from a systematic review of available genotype to phenotype literature. The database is released along with an R package to provide a low barrier of entry to variant resistance annotation and clinical implication analysis from common sanger and NGS sequence data. This represents the first openly available and community maintainable knowledgebase of drug resistance mutations for the human herpes viruses (HHV), developed for the community of researchers and clinicians tackling HHV drug resistance. AvailabilityThe HerpesDRG database is available at github.com/ojcharles/herpesdrg-db. The R package for resistance genotyping data is available at github.com/ojcharles/herpesdrg. A user-friendly webserver is available at cmv-resistance.ucl.ac.uk/herpesdrg

bioinformatics↗