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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