Please enable JavaScript.
Coggle requires JavaScript to display documents.
MFOLD (PARAMETERS) (METHODOLOGY (Enter the sequence name., Enter the…
MFOLD (PARAMETERS)
METHODOLOGY
-
-
- Check
☑
the ss-count for color annotation
- Remain all other setting default
-
Excise
ClosedExcise
excludes the sequence range from base i+1 through base j-1 from folding, forcing a base pair between the bases i and j.
can exclude up to 9 regions from folding in this manner by specifying sequential numbers with the -CLOSedexcise parameter (-CLOSedexcise1=i,j ... -CLOSedexcise9=y,z).
The only allowable base pairs are A-T/U, G-C, and G-T/U. Attempts to force other base pairing produce undefined results.
OpenExcise
excludes the sequence range from base i through base j from folding, "ligating" base i-1 to j+1 before folding the molecule.
can exclude up to 9 regions from folding in this manner by specifying sequential numbers with the -OPENexcise parameter (-OPENexcise1=i,j ... -OPENexcise9=y,z).
-
-
Temperature
lets you select the folding temperature in degrees Celsius. The default folding temperature is 37 degree
-
MAX Loop size
set the maximum size for an interior or bulge loop in the predicted secondary structures. An interior loop is an unpaired region interrupting a helix, with unpaired bases on both strands of the interrupted region. A bulge loop is a loop-out in a helix involving only one of the helix strands. The size of the loop is the total number of unpaired bases in the loop.
LOPsidedness
sets the maximum lopsidedness for an interior or bulge loop in the predicted secondary structures. For an interior loop, this is the maximum difference between the number of single-stranded bases on one side of the loop and the number of single-stranded bases on the other side. For a bulge loop, this is the maximum number of bases in the loop.
Monitor
shows the progress of MFold on your screen. Use this parameter to see this same monitor in the log file for a batch process. If the monitor is slowing down the program because your terminal is connected to a slow modem, suppress it by including -NOMONitor on the command line
Summary
writes a summary of the program's work to the screen when you've used -Default to suppress all program interaction. A summary typically displays at the end of a program run interactively. You can suppress the summary for a program run interactively with -NOSUMmary.
Batch
submits the program to the batch queue for processing after prompting you for all required user inputs. Any information that would normally appear on the screen while the program is running is written into a log file. Whether that log file is deleted, printed, or saved to your current directory depends on how your system manager has set up the command that submits this program to the batch queue. All output files are written to your current directory, unless you direct the output to another directory when you specify the output file.
Force
forces the helix that begins with the base pair between bases i and j and extends for k bases to the base pair between i+k-1 and j-k+1.
Prevent
prevents the helix that begins with the base pair between bases i and j and extends for k bases to the base pair between bases i+k-1 and j-k+1.