Similarity score calculation methods and their parameters.
Datasets usually provide raw data for analysis. This raw data often comes in spreadsheet form, but can be any collection of data, on which analysis can be performed.
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.