MFOLD on Helix
MFOLD
performs RNA and DNA secondary structure prediction using nearest
neighbor thermodynamic rules. It can accept input in Genbank, GCG
and Fasta formats. MFOLD was developed by Dr. Michael Zuker at RPI.
[MFOLD website]
How to Use
MFOLD can be run in two ways on the Helix Systems:- Web interface
- Command line (see sample session below)
Version
The screen output from MFOLD includes the version number (see the sample session for an example).Sample Session (user input is in bold)
<helix>% ls a00006.fasta <helix>% mfold SEQ=a00006.fasta ___ _ _ /'___) (_ ) ( ) ___ ___ | (__ _ | | _| | /' _ ` _ `\| ,__)/'_`\ | | /'_` | | ( ) ( ) || | ( (_) ) | | ( (_| | (_) (_) (_)(_) `\___/'(___)`\__,_) ___ __ _ /'_ ) /'__`\ _ _ __ _ __ ___ (_) _ ___ (_)_) | (_) ) ) ( ) ( ) /'__`\( '__)/',__)| | /'_`\ /' _ `\ _(_ < /' / | \_/ |( ___/| | \__, \| |( (_) )| ( ) | ( )_) | _ /' /( ) `\___/'`\____)(_) (____/(_)`\___/'(_) (_) `\____)(_)(_____/' /usr/local/bin/mfold: line 81: cd: a00006.fasta: Not a directory REUSE= NO a00006.pnt created. Sequence length is 26 Folding at 37 degrees using version 3.0 dat files. 10,20, End of Fill Save file created using nafold2. Minimum folding energy is -9.9 kcal/mole. Energy increment is 1.0 kcal/mole. H-num file created from plot file. 1, Suboptimal foldings created. Energy dot plot created. Free energies re-evaluated using efn2 and added to ct file. sir_graph_ng Rotation angle: 0.00 degrees Input File: a00006_1.ct Sequence length: 26 Using 356.0 degrees of the circle Output: a00006_1.ps ss file output is a00006_1.ss Normal exit from sir_graph_ng Structure plots generated. All done. <helix>% ls a00006-local.seq a00006.fasta a00006.log a00006.ps a00006_1.ct a00006_1.ss a00006.ann a00006.gifdat a00006.out a00006.rnaml a00006_1.jpg a00006.ct a00006.h-num a00006.plot a00006.sav a00006_1.pdf a00006.det a00006.jpg a00006.pnt a00006.ss-count a00006_1.ps
Output
As seen in the example above, Mfold creates many output files from a single run.- filename.log -- log of the calculations.
- filename*.gif -- gif images of the proposed structures. (see images below)
- filename*.ps -- Postscript files of the proposed structures
Documentation
MFOLD documentationSample MFOLD outputs: