RSEARCH: Finding homologs of single structured RNA sequences

BMC Bioinformatics

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

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

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.

ISSN: 1471-2105