Rapid screening and detection of inter-type viral recombinants using phylo-k-mers.

ABSTRACT:

Motivation

Novel recombinant viruses may have important medical and evolutionary significance, as they sometimes display new traits not present in the parental strains. This is particularly concerning when the new viruses combine fragments coming from phylogenetically distinct viral types. Here, we consider the task of screening large collections of sequences for such novel recombinants. A number of methods already exist for this task. However, these methods rely on complex models and heavy computations that are not always practical for a quick scan of a large number of sequences.

Results

We have developed SHERPAS, a new program to detect novel recombinants and provide a first estimate of their parental composition. Our approach is based on the precomputation of a large data

SUBMITTER: Scholz GE 

PROVIDER: S-EPMC8016494 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature