Table 2

Default scoring parameters (can be arbitrarily weighted or changed by user defined settings).

parameter

default value

protein scores

BLOSUM62 ×50

nucleic acid scores

identity 1000, else 300

gap open penalty

-1500

gap extension penalty

-300

Remark. The effect of the positive default score for nucleic acid mismatches is to reduce the influence of nucleic acid mismatches relative to the amino acid and gap scores.

Stocsits et al. BMC Bioinformatics 2005 6:160   doi:10.1186/1471-2105-6-160