Figure 7

Multiple structure alignment and iterative database search. (A) Flowchart of multiple structure alignment and iterative database search. Step (1a) accepts a query structure to start an iterative database search; step (1b) processes a small database for multiple structure alignment; step (2) derives a profile from the seed alignment; step (3) uses the profile to conduct search; and step (4) updates the profile with new alignment. (B) Multiple structure alignment of several IRE structures. (C) PSSM of the multiple alignment of IRE in (B). Each column in the PSSM corresponds to the position of a structure component, either single base or base pair. Position of a single base is represented by the nucleotide number and position of a base pair is represented by two nucleotide numbers connected by a dash. For each column, the scores of individual structure components in that position are listed in rows where "-" means not applicable.