Simply double click on the self-extracting file Circles.exe and follow the instructions.
Circles does two main things:
For the first task, Circles can import a sequence alignment, ask you to specify the options for the MWM analysis, then run the command line programs. You can then display the results as circle plots. You can extract the largest possible planar RNA structure form these circle plots, and save it in a number of formats that can be display by other programs, such as those listed here.
Perhaps the best way to learn how to use the program is to actually use it, so please work through this tutorial.
Use the File | Import command to read in a set of aligned sequences in either FASTA, ClustalW, or NEXUS format (don't use the Open command to do this, it won't work!). The program will display the sequences in a sequence window. At present you cannot edit the alignment. The program comes with the file Hickson.fas, which contains an alignment of mitochondrial 12S rRNA sequences in animals.
Go to the Structure menu and choose Maximum weight matching. You are presented with a dialog box listing the options for the analysis:
MWM can be computed from two different sources of information, mutual information and helix plot scores. You can decide to use either one or the other, or both sources of information. There are various options determining how the scores are computed, and if you use both mutual information and helix plot scores you can specify the relative weights you want to give each source. At any time clicking on the Defaults button will restore the default settings.
The results of the MWM analysis are a list of the base pairs that together have the greatest weight. This file is written to the Windows temporary directory (typically this is C:\WINDOWS\TEMP). To view these pairings, chose Circle plot from the Structure menu. You will be asked to select from a list of sequences. The program will then display a circle plot of the pairings for the sequence. You can toggle between two different styles of drawing the pairings, and whether you want the bases displayed or not.
In a circle plot the RNA sequence is depicted as a circle and the base pairs by lines or chords connecting pairs of bases. Helices are indicated by sets of parallel chords (lines). If the lines overlap then this may be evidence of a psuedoknot, or it may be due to weak or conflicting evidence for different helices.
The circle plot includes only those pairings that have at least one neighbouring pair (i.e., lone pairs are excluded). You may want to explore these lone pairings. There may also be pairs in the original MWM that you might think are spurious and should be removed. You can do this using the Add/Remove lone pairs and Edit base pairs commands, respectively. In each case you are given a dialog box in which you can select the pairs you want to include in the plot. Use Shift- and Ctrl-clicking to make multiple selections. Any change you make is instantly shown in the circle plot.
RNA secondary structure is typically represented as a planar graph (i.e., a graph where no pair of edges overlap). For very clean alignments the MWM may already be planar, but often it won't be. To generate a secondary structure from the MWM you can extract the largest planar structure using the command Structure | Maximum loop matching. You will see the following dialog:
Two options available are whether you want to find the structure for just the original MWM pairings, or those currently displayed. If you haven't edited any pairings (step 4 above) then the two options are be the same and the radio buttons are disabled. The largest planar structure is extracted using an algorithm by Nussinov et al.-- Durbin et al give a nice discussion of this algorithm in chapter 10 of their book "Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids."
Circles doesn't display secondary structures, so to save the structure displayed in a circle plot window, choose Export structure from the Structure menu. Circles supports the following formats:
|MFOLD connect file||Standard format produced by secondary structure prediction programs, and Michael Zuker's MFOLD server|
|Olsen LOOPSOL||Simple nested parentheses format that can be displayed by loopDloop|
|DCSE alignment||Format used by the DCSE alignment editor. Structure can be displayed by the program RnaViz.|
If you prefer you can use Jack Tabaska's programs from the command line. If you do this, you may make use of the Perl script toXRNA.pl that takes an alignment and matching, and outputs files for the UNIX program XRNA. Circles can read these files and produce a circle plot, which can then be analysed as in steps 3-6 above.
Use the File | Open command to open the primary sequence file (*.pri). Circles will read that file, and expects to find the base pairing (*.bp) and lone pairs (*.lone) files in the same directory. It will then display a circle plot.
You can now proceed as Steps 3-6 above to get a secondary structure.
Other commands are being added to Circles. Some may be on the menus but permanently disabled. This means that they are currently being tested. At present the following additional commands are available.
If the matching analysis takes a little time, then rather than recompute the matching every time you open your alignment file you can load the last matching using the Load imatch file command. You will be pormpted to open the file circle.im in the Windows temporary directory. Becuase this file is overwritten with each MWM analysis, it will only be valid if it was computed from the same alignment file.
Circles was developed using Borland C++ 5.01. The program makes use of Paul Lewis' Nexus Class Library.
[Back to Circles home page]