Experimental validation of in silico predicted RAD locus frequencies using genomic resources and short read data from a model marine mammal.

ABSTRACT:

Background

Restriction site-associated DNA sequencing (RADseq) has revolutionized the study of wild organisms by allowing cost-effective genotyping of thousands of loci. However, for species lacking reference genomes, it can be challenging to select the restriction enzyme that offers the best balance between the number of obtained RAD loci and depth of coverage, which is crucial for a successful outcome. To address this issue, PredRAD was recently developed, which uses probabilistic models to predict restriction site frequencies from a transcriptome assembly or other sequence resource based on either GC content or mono-, di- or trinucleotide composition. This program generates predictions that are broadly consistent with estimates of the true number of restriction sites obtained th

SUBMITTER: Vendrami DLJ 

PROVIDER: S-EPMC6341687 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature