Open AccessRapid screening and detection of inter-type viral recombinants using phylo-k-mers
Author(s) -
Guillaume E. Scholz,
Benjamin Linard,
Nikolai Romashchenko,
Éric Rivals,
Fabio Pardi
Publication year - 2020
Publication title -
bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.599
H-Index - 390
eISSN - 1367-4811
pISSN - 1367-4803
DOI - 10.1093/bioinformatics/btaa1020
Subject(s) - context (archaeology) , phylogenetic tree , source code , biology , computer science , computational biology , genome , task (project management) , genetics , gene , programming language , paleontology , management , economics
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.