Allow UNAfold.pl To Process files with multiple sequences for processing

2 replies [Last post]
ahammouda
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Joined: 12/23/2011

Hello,

I want to start by thanking you for making your software freely available online. I've really enjoyed playing with it. I was wondering why UNAfold.pl doesn't seem to be set up to allow multiple sequences from the same file to be processed. Was this a design decision, or is it a function that is just waiting to be suggested?

Cheers

boas1002
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Joined: 03/18/2012
I also was pleased with this

I also was pleased with this software. Hopefully continue to be developed into a better and easier to use.

zukerm
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Joined: 11/12/2010
The UNAFold.pl script was

The UNAFold.pl script was created as an afterthought. It mimics the behavior of the mfold script from the mfold software suite. It folds a single-sequence but produces elaborate output for that sequence. It also computes partition functions, yielding stochastic samples of structures and probability dot plots that give the probability of all base pairs. The hybrid2.pl script accepts one or two sequences as input and computes melting profiles for them. There are many other scripts that can be written. Our philosophy was that the user should create or modify Perl scripts to satisfy requirements. I realize that this is an unrealistic expectation for a typical user.

The quikfold application on the web server is an example of an application that folds many sequences from a single file. It predicts minimum free energy foldings and suboptimal foldings. The program that does this is called hybrid-ss-min. If the file 'RNAs.seq' contains multiple RNA sequences in FASTA format, then the command

hybrid-ss-min --suffix=DAT --mfold RNAs.seq

will give you mfold style foldings of all the sequences using default values for P, W, and MAX. RNA version 3.0 energies will be used. You would then have to process the resulting ct file into individual structures and run these through a drawing program. Individual ct files can be uploaded to the Structure display and Free Energy Determination application.

I was hoping that individual members of this forum would write such applications and deposit them with us for distribution to all. This has not happened so far. You are correct in suggesting that this would be a welcome addition. Try using the quikfold application on the server. See what it does. It this satisfactory? What other types of output would you like to see?