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Table 1 All possible node-states and their emission scores.

From: RSEARCH: Finding homologs of single structured RNA sequences

Node-state Description Profile emission score Single-sequence emission score Gap class
ROOT_S Start of model 0 0 M_cl
ROOT_IL Gap in query at left end 0 IL_cl
ROOT_IR Gap in query at right end 0 IR_cl
BEGL_S Start of left branch of bifurcation 0 0 M_cl
BEGR_S Start of right branch of bifurcation 0 0 M_cl
BEGR_IL Gap in query at bifurcation 0 IL_cl
MATP_MP Matched base pair M_cl
MATP_ML Match on left side of base pair; gap in target on right S aj DR_cl
MATP_MR Match on right side of base pair; gap in target on left S bj DL_cl
MATP_D Two gaps in target, for each side of base pair 0 0 DB_cl
MATP_IL Gap in query just after left side of base pair 0 IL_cl
MATP_IR Gap in query just before right side of base pair 0 IR_cl
MATL_ML Match to single nucleotide on left S aj M_cl
MATL_D Gap in target on left 0 0 DL_cl
MATL_IL Gap in query on left 0 IL_cl
MATR_MR Match to single nucleotide on right S bj M_cl
MATR_D Gap in target on right 0 0 DR_cl
MATR_IR Gap in query on right 0 IR_cl
END_E End of stem-loop 0 0 M_cl
BIF_B Bifurcation 0 0 M_cl
  1. v is the current state. a is the nucleotide present in the query on the left, b is the nucleotide present in the query on the right. j is any nucleotide in the target for a single nucleotide alignment, while k, l is a base pair in the target for a base pair alignment. g is the background frequency of a nucleotide and s and s' are the substitution matrices defined in the text. Node-states with an M gap class are in the "mainline" path through the model that the an exact match would follow. Node-states with an IL or IR gap class represent a gap in the query sequence, while node-states with a DL, DR, or DB gap class represent gaps in the target sequence.