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Table 2 Parameterization of negative transition scores from gap penalties.

From: RSEARCH: Finding homologs of single structured RNA sequences

  To class
From class M_cl IL_cl DL_cl IR_cl DR_cl DB_cl
M_cl 0 1/2α 1/2α 1/2α 1/2α α
IL_cl β + 1/2α β β + α β + α β + α β + 3/2α
DL_cl β + 1/2α β + α β β + α β + α β + 1/2α
IR_cl β + 1/2α N.A. β + α β β + α β + 3/2α
DR_cl β + 1/2α β + α β + α β + α β β + 3/2α
DB_cl 2β + α 2β + 3/2α 2β + 1/2α 2β + 3/2α 2β + 1/2α
  1. α and β are replaced with α' and β' for the specific cases described in the text. The IR_cl to IL_cl transition is never allowed in these models.