RNALOSS: a web server for RNA locally optimal secondary structures

Abstract

RNAomics, analogous to proteomics, concerns aspects of the secondary and tertiary structure, folding pathway, kinetics, comparison, function and regulation of all RNA in a living organism. Given recently discovered roles played by micro RNA, small interfering RNA, riboswitches, ribozymes, etc., it is important to gain insight into the folding process of RNA sequences. We describe the web server RNALOSS, which provides information about the distribution of locally optimal secondary structures, that possibly form kinetic traps in the folding process. The tool RNALOSS may be useful in designing RNA sequences which not only have low folding energy, but whose distribution of locally optimal secondary structures would suggest rapid and robust folding. Website: http://clavius.bc.edu/~clotelab/RNALOSS/.

Figure 1

Screen image of web server RNALOSS. Users may input an RNA sequence consisting of upper or lower case nucleotides A, C, G, T, U, either by uploading a FASTA-format file (A) or by pasting a nucleotide sequence into (B).

Figure 2

Output of web server RNALOSS on type III hammerhead ribozyme AF170517 from Rfam (24). The web server RNALOSS outputs a table of number of k-locally optimal secondary structures, for each possible value of k ≥ 0 (shown here). Additionally, tables for the relative density of states and mfe values of sample k-locally optimal secondary structures are displayed in the browser (data not shown).

Figure 3

Column graph of relative density of states is obtained by clicking a hot link from the previous screen shot. For each value of k ≥ 0, the ratio of number of k-locally optimal secondary structures over the total number of locally optimal secondary structures is displayed.