How to visualize mfold output files?

[mbochert]

Hi, Im a PhD student at UIUC in the molecular and cellular biology department. I've recently downloaded and ran mfold 3.6 from the terminal, however I'm unsure what to make of the output files (.ps , .ct , etc.). I see that there is a program called PlotFold that will allow for the visualization of these files, however I don't know where to find it.. Are there any programs that you recommend to use in order to visualize these files?

Thanks,

Michael

[zukerm]

Suppose that the name of your sequence file is myRNA.seq. Then doing the simple:

mfold SEQ=myRNA.seq

will produce a number of files. myRNA.out gives a crude visualization of the folding(s). Assuming that you installed the software correctly, there should also be files named myRNA_1.ps, myRNA_2.ps and so on depending on the number of secondary structures predicted. The '.ps' suffix means that the file is a PostScript. They contain plots of the secondary structures. You need a PostScript viewer on your computer. You should also have files with the suffix '.pdf' that can be visualized using, for example, Adobe Reader. 'pdf' stands for 'Portable Document Format'. What is in the log file? In this case, it would be myRNA.log. You can upload single '.ct' files to:

http://www.unafold.org/mfold/applicatio ... nation.php

Be patient, it might take a long while for the computation to complete.

I suggest you read: http://www.unafold.org/doc/mfold-manual/
and look at
http://www.unafold.org/mfold/documentat ... rences.php