Find Resistance with ShortBRED is unable to detect approximately 27% of markers in the QMI-AR Peptide Marker Database (7.0) when using default settings. The missed markers are primarily short peptides fewer than 12 amino acids in length.
An improved detection rate can be achieved by setting a loose e-value; however, 15% of markers in the database remain undetected even when present.
The Find Resistance with ShortBRED abundance table may report abundance values of zero for the affected markers, suggesting their absence in your data, when in fact, these markers were present but went undetected by the software.
This issue affects CLC Microbial Genomics Module and CLC Microbial Genomics Server Extension 24.1.1 and earlier.
