The predicted C. ulcerans proteins were mapped onto the SBML templates by means of bidirectional best BLASTP hits using the scoring matrix BLOSUM62 and the user-defined E-value cutoff of 1 × 10-10.
Probe candidates passing the criteria (e.g., Tm cutoff, GC%, the proximity of 3' end, in silico hybridization (sequence complexity and homology to non-target sequence), are ranked by the E-value of the probe-target duplex (blastn) using the scoring matrix built from the customized reference sequence.
The molecular-dynamics based method used the scoring matrix in Table 1, and the contact map method used the scoring matrix in Table 2.
The allelic data were converted into a binary matrix using the scores 1 or 0 for the presence or absence of the peak.
Different designs were generated using the original sensitivity matrix, the score matrix as well as using a space-filling design and performing a sequential approach.
For ribosomal RNA genes, the Q-INS-i algorithm (which considers secondary RNA structure) was used with the scoring matrix set to 1PAM/k = 2, gap penalty = 1.53, and offset value = 0.1.
Dot-matrix comparisons were performed using the Blosum90 scoring matrix.
Therefore, the distribution of alignment scores is likely different for consensus and native sequences, at least when using the same scoring matrix for both [such as BLOSUM62 (Henikoff and Henikoff, 1992) or the corresponding position-specific scoring matrices].
Third, we use this score matrix to determine the similarity between strains, and cluster them using a stable version of k-means.
Using the appropriate scoring matrix during the BLAST search (among available BLOSUM and PAM standard matrices) can improve AnABlast sensitivity.
