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

For more information about the other files produced, see the Output section of the Mfold documentation.

Documentation

MFOLD documentation

Sample MFOLD outputs:

Helix Systems Scientific Supercomputing at the NIH