HOTSPOT: hierarchical host prediction for assembled plasmid contigs with transformer.

ABSTRACT:

Motivation

As prevalent extrachromosomal replicons in many bacteria, plasmids play an essential role in their hosts' evolution and adaptation. The host range of a plasmid refers to the taxonomic range of bacteria in which it can replicate and thrive. Understanding host ranges of plasmids sheds light on studying the roles of plasmids in bacterial evolution and adaptation. Metagenomic sequencing has become a major means to obtain new plasmids and derive their hosts. However, host prediction for assembled plasmid contigs still needs to tackle several challenges: different sequence compositions and copy numbers between plasmids and the hosts, high diversity in plasmids, and limited plasmid annotations. Existing tools have not yet achieved an ideal tradeoff between sensitivity and preci

SUBMITTER: Ji Y 

PROVIDER: S-EPMC10159655 | biostudies-literature | 2023 May

REPOSITORIES: biostudies-literature