Figure 1.
The FASTA/plain text RNA primary sequence ran by RNAL fold and compared with known IRES structure by RNA Align and pknotsRG programs. The IRES structures are displayed by RnaViz software and alignment results can be edited by any text editor. The eight private programs are pointed beside arrow symbols. The sort codes are shown in Supplementary file (Methods S1).
Figure 2.
The distribution of R and pseudoknot parameters from positive and negative group of four IRES groups by VIPS analysis.
The distribution of four IRES groups calculated by R and pseudoknot parameters in positive group and negative group. The R scores and pseudoknot scores were demonstrated according to IRES group 1 (a and e), IRES group 2 (b and f), IRES group 3 (c and g) and IRES group 4 (d and h). Linear discriminant analysis was applied to determine the cut-off line of the R score in each group shown as (a), (b), (c) and (d). Distribution of positive and negative IRES elements that were calculated and summarized from R and pseudoknot values are shown as (e), (f), (g) and (h).