Table_2.xls (21.5 kB)

Similarity score calculation methods and their parameters.

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posted on 30.11.2010 by Adrian Schröder, Johannes Eichner, Jochen Supper, Jonas Eichner, Dierk Wanke, Carsten Henneges, Andreas Zell

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.

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