Figure 11
From: Structator: fast index-based search for RNA sequence-structure patterns
An example of local chains of RSSP matches. (A) Consensus secondary structure visualized with the VARNA program of the HAR1F RNA family showing stem-loops HP1, HP2, and HP3. (B) SSD consisting of RSSP1, RSSP2, and RSSP3 in Structator syntax describing the three stem-loop regions of HAR1F. (C) Regions of HAR1F described by the RSSPs, including distances li+1- r
i
, 1 ≤ i < 3, between neighbored RSSPs and RSSP weights α(RSSP
i
), 1 ≤ i ≤ 3. (D) Examples of local chains 
, 1 ≤ i ≤ 4 found with the SSD, showing, in each chain, the distance between RSSP matches and their local chain score 
. Gap cost computation according to Equation (4) is shown exemplary for the two RSSP matches of chain 
.