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Table 5 Description of optimized parameters derived for each method used herein.

From: Searching for evolutionary distant RNA homologs within genomic sequences using partition function posterior probabilities

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