The post-processed information is then given to a new dynamic programming routine that produces an optimally segmented consensus secondary structure for each of the multiple alignment sequences.
The consensus secondary structure of the described ncRNA family was determined using RNAalifold (PMID: 12079347).
A consensus secondary structure prediction sequence was drawn from the results of the different secondary structure prediction servers (Fig. S2).
Consensus secondary structure propensity was determined based on SSPro [34], Jpred [35], GOR IV, SOPMA and HNN [36].
The consensus secondary structure prediction showed that the PvTRAg33.5 has 76.2% helix and 23.8% coil with no extended sheets.
The consensus secondary structure was derived employing the probability of the predicted sequence and the type of secondary structure prediction from these methods.
Mapping of these two sites on the consensus secondary structure for mammalian mitochondrial 12S rRNA showed that they are located in the 3' minor domain [7].
Knowledge about conformational preferences and structural regularities, going beyond the primary sequence is captured by the consensus secondary
The highly stable consensus secondary structure of this family of ncRNAs is evident (Fig. 4) and the expression of two members (lpr0049 and lpr0069) was confirmed by Northern Blot (Fig. 2).
To assess the structural implications of these variants, we modeled their secondary structures based on consensus secondary structures of the mammalian mitochondrial tRNAs [8]. Figure 2 shows our secondary structure models for all the five tRNA genes.
Consensus secondary structures were predicted using the JPred program [ 155].
