Similarity score calculation methods and their parameters.
2010-11-30T01:52:45Z (GMT) by
<p>For each feature the method, its parameters and, when needed, the substitution matrix are provided. The parameters and give the gap opening and gap extension penalties and gives a similarity distance threshold below which two amino acids are still considered a match. The parameters and , are parameters of the local alignment and mismatch kernel, respectively. The parameter defines the length of the flanking regions considered for the alignment.</p>