Double stranded DNA modeling

Joe Ryan jfryan at NHGRI.NIH.GOV
Tue Jun 29 10:10:00 EST 1999


> Does anyone know of  a programme for predicting the 3D structure of
> double-stranded DNA.

These programs are part of the GCG Package.
you can also submit MFold jobs via www at http://mfold.burnet.edu.au/

MFold
     MFold predicts optimal and suboptimal secondary structures for an RNA
     or DNA molecule using the most  recent  energy minimization method of
     Zuker.
PlotFold
     PlotFold displays the optimal and suboptimal secondary structures for
     an RNA or DNA molecule predicted by MFold.
StemLoop
     StemLoop  finds  stems (inverted  repeats) within  a  sequence.   You
     specify the minimum stem length, minimum and  maximum loop sizes, and
     the minimum  number  of bonds  per stem.   All stems or only the best
     stems can be displayed on your screen or written into a file.
DotPlot
     DotPlot  makes  a  dot-plot with  the output  file  from  Compare  or
     StemLoop.

Good Luck,

Joe
--
Joseph Ryan
Programmer
National Human Genome Research Institute




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