[Bio-software] Help with RNA folding software

rtarrial rtarrial at gmail.com
Tue Aug 8 13:40:48 EST 2006


Hi all,
I´m a newbie to RNA folding software, needing all the help I can get.
My approach is to identify a transcriptome on various aspects, one of
them is the free energy of the transcripts.
As this is a initial large-scale screening, my major interest is on the
free energies (numerical variables) and not on the structure generated.
Reading the literature related to calculating RNA folding, I found the
new algorithm Afold (Roytberg et al, 2006), to be the most suitable to
this approach, as it is fast and directed to genomic analyses.
But, as I mentioned, I´m a total newbie to the topic, but nevertheless
downloaded the program (ftp://ftp.ncbi.nlm.nih.gov/pub/ogurtsov/Afold)
and ran it on some of my sequences. I´m ashamed to say this, but I
wasn´t even able to read the output :/
Here is a small portion of the output I´ve got:

..G..1..1126..U.. = -253.20 Multidomain
..G..1..1126..U.. = -253.20 0x0
..A..2..1125..U.. = -247.30 internal
..U..9..1116..A.. = -251.50 0x0
..C..10..1115..G.. = -249.10 0x0
..C..11..1114..G.. = -245.80 0x0
..A..12..1113..U.. = -243.70 multi
..U..15..632..A.. = -143.00 0x0

My question is, is there any way to extract only the delta-G´s of the
analysed sequences, ignoring the structure generated? Any program to
read this output? There´s no documentation accompanying the program,
nor any instructions on the paper, guess they suppose the user already
knows how to use it, which obviously is not my case.. I´m planning to
use it on up to 10,000 sequences. I´ve also got some knowledge on Perl
programming,.

Any help would be greatly appreciated!!

Roberto




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