How to use concentrations(-same).pl in UNAFold package

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tnwl124
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Joined: 04/03/2015

I use UNAFold package version 3.8.

I can use hybrid2.pl that use concentration, concentrations.pl, hybrid, hybrid and so on ....

The hybrid2.pl make the Tm graph about self hybridization for one sequence or hybridization for two sequence and the Tm graph is made by gnuplot to use gp file(file_name.gp).

but, I need Tm graph about ssDNA folding related with the result from UNAFold.pl or hybrid-ss-min or hybrid-ss.

Solving this problem, I repeatedly read UNAFOld manual.

Eventually I find that the gp file is made by concentrations(-same).pl.

But the manual is not included directions about concentrations(-same).pl.

So, I try to know how to use concentrations(-same).pl.

In the terminal(I use Ubuntu), I input the command "concentrations.pl" and "concentrations-same.pl"

the result is "Usage: /use/bin/concentrations(-same).pl prefix".

Or I input the command "concentrations.pl -h" and "concentrations-same.pl"

the result is "No such file or directory does not exist at/usr/bin/concentrations.pl line 15."

I go to usr/bin . there exist the concentrations.pl and concentrations-same.pl.

I don't know how to use concentrations(-same).pl ....

please help me.....

NMarkham
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Joined: 09/29/2011
concentration.pl and

concentration.pl and concentration-same.pl don't create .gp files; hybrid2.pl does that. In fact, concentration(-same).pl do very little on their own, and I really can't think of a scenario where it would make sense to call them directly.

One possible solution is to run hybrid2.pl with the same sequence file specified twice (to simulate a one-sequence ensemble) and use the "--exclude=AA" option to exclude the homodimer, so that the only species considered is the monomer. The resulting concentration plot will be very uninteresting (since the only possible conformation is 100% single-stranded!) but the other plots should have some information.