BioLaboro: A bioinformatics system for detecting molecular assay signature erosion and designing new assays in response to emerging and reemerging pathogens

Mitchell Holland; Daniel Negrón; Shane Mitchell; Nate Dellinger; Mychal Ivancich; Tyler Barrus; Sterling Thomas; Katharine W. Jennings; Bruce Goodwin; Shanmuga Sozhamannan

Discovery of potential new BOMV assays using BioLaboro end-to-end pipeline 204 Using BioLaboro we ran a New Assay Discovery job to discover new BOMV signatures 205 and determine their potential for accurate detection using PSET. In the first phase, BioVelocity 206 was used to search for conserved and signature regions within the selected genomes. We selected 207 the organism of interest by searching for "Bombali ebolavirus" from the database and selecting 208 the three available complete genomes. The MF319185.1 genome was used as the algorithmic 209 reference sequence as it is the same one that NCBI selected for the RefSeq database (Genbank 210 ID: NC_039345.1). The algorithmic reference sequence was first split into k-mers of 50 bps each 211 using a sliding window of 1 bp, which amounts to 18,994 k-mers to be evaluated with 212 BioVelocity's conserved sequence detection algorithm. BioVelocity found 27% (5,237) of these 213 k-mers to be conserved in all three of the BOMV genomes. The conserved k-mers were then 214 evaluated to determine overlapping segments and were combined into 120 conserved contigs.