Table 5

Description of optimized parameters derived for each method used herein.

Method

Scoring matrix

Gap opening penalty

Gap extension penalty

Probalign

+5/-4 (T = 7)

32

2

SSEARCH

+5/-4

10

4

ClustalW

+10/-9

13

6

BLAST

+5/-4

8

6

Roshan et al. BMC Bioinformatics 2008 9:61   doi:10.1186/1471-2105-9-61