Brian Thomas Foley

Hypermut 3: Identifying specific mutational patterns in a defined nucleotide context that allows multistate characters

Hypermut 3 detects hypermutation patterns in sequences, handling multistate characters and gaps, and is available as a web and command-line tool.

Reference plasmid pHXB2_D is an HIV-1 molecular clone that exhibits identical LTRs and a single integration site indicative of an HIV provirus

The paper compares long-read nanopore DNA sequencing with short-read sequencing for full-length HIV-1 provirus analysis, finding full coverage and variants in a reference plasmid.

Botulinum-neurotoxin-like sequences identified from an Enterococcus sp. genome assembly

The paper identifies a botulinum-neurotoxin-like gene cluster in an Enterococcus sp. genome, similar to known BoNT gene clusters but with unknown pathogenic potential.