The interface | How to make a definition file | How to read the results | Riboswitch references
Denison Riboswitch Detector (DRD) is an online tool that uses a motif-finding algorithm to find riboswitches within a DNA sequence. The specific motif, along with other parameters of the algorithm, can be chosen from a set of predefined motifs or can be changed by creating a new definition file (see How to make a definition file below).
A definition file is a simple text file with information about the desired motifs for a search.
The algorithm first breaks the sequence into short segments and searches each segment for a riboswitch. So the definition file begins with two numbers defining the length of these segments and the overlap between segments.
The next line contains the number of motifs in the riboswitch, followed by one line per motif. Each motif line contains the motif itself followed by the minimum number of identities necessary for this motif to be detected by the algorithm.
Following the motifs is one line containing maximum distances between motifs. The first number in this line is the number of bases added to a putative riboswitch before the first motif. The next number is the maximum distance between the first and second motifs, followed by the maximum distance between the second and third motifs, etc. The last number is the number of bases added to a putative riboswitch after the last motif.
The next line contains minimum distances between motifs. The first number is the minimum distance between the first and second motifs, followed by the minimum distance between the second and third motifs, etc.
The next line contains the minimum number of total identities, from all motifs, for a result to be considered a match, followed by the minimum number of identities in a global alignment of Vienna strings, followed by the maximum length of a putative riboswitch.
This is followed by a Vienna string describing the consensus secondary structure of the riboswitch. The last line in the file is this consensus secondary structure with the motifs inserted at the appropriate positions, used to more accurately align the secondary structure of a putative riboswitch with the consensus.
The Vienna alignment score is computed from a global alignment between the consensus Vienna string with motifs inserted and the Vienna string of a putative riboswitch with motifs inserted. The values of the scoring matrix are set as follows, to encourage motifs to align:
|mismatch base and parenthesis||-3|
|open a gap||-1|
|extend a gap||0|
When Submit is pressed, work begins and a results window appears for each selected riboswitch describing the progress so far. The pages will refresh every three seconds, leading ultimately to the final results, listed in order of motif identity score, then Vienna identity score. In our tests, matches to previously annotated riboswitches were virtually always displayed on top. Clicking on a result sets up a BLAST query. Below the alignments and scores, optimal and suboptimal secondary structures computed by mFold are displayed with the Rfam consensus image.
If you find this server useful, please cite:
J.T. Havill, C. Bhatiya, S.M. Johnson, J.D. Sheets, and J.S. Thompson. A new approach for detecting riboswitches in DNA sequences. Bioinformatics 30(21):3012-3019, 2014.
Department of Mathematics and Computer Science