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Anyone familiar with I-Tasser manish Bioinformatics 0 04-04-2011 11:15 PM

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Old 04-01-2011, 12:26 AM   #1
holywoool
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Lightbulb Anyone familiar with RNAFold?

Hi,
I'm using RNAFold software to predict RNA secondary structure.I'm not sure the optimized range of RNA sequence with which RNAFold shall output best result.
At present,the sequences are at length 4001bp,maybe it is too long for RNAFold to yield best results.
Any suggestion shall be appreciated!
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Old 04-01-2011, 08:06 PM   #2
kvarala
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Default Which kind of RNA?

Which kind of RNA are you trying to identify? 4000 bp is obviously too long for miRNA. I am not sure what the correct length would be for rRNA. Perhaps you can look at known rRNA molecules and compute the average length from those examples. Good luck.
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Old 04-01-2011, 10:51 PM   #3
holywoool
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Thanks,
The RNAs are pre-mRNA,and the lengths vary from several thousand to several hundred thousand nt.At present,RNAFold can predict sequence upto 10000bp,however the accuracy may decrease as the sequence grows.I'm wondering whether at length 4001bp can RNAFold work with high performance.Because I need to find double-strand regins within 4001bp pre-mrna sequence.
Thanks again!
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Old 04-04-2011, 07:48 PM   #4
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Hi holywoool,

RNAfold is not the right tool for this. It will try to compute an optimal structure over the whole sequence length. The performance and runtime of RNAfold (and other global structure prediction tools) decreases rapidly once you get over say 1000bp (can dig out a few references for this if needed).

You could however use RNAplfold or RNALfold (part of the Vienna RNA package, just as RNAfold) or Rfold. They predict *local* RNA structures in a sliding window fashion. Those predictions are more accurate for long sequences.

But I'm sure there are more specialised tools for finding special structures...

Andreas
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Old 09-06-2011, 03:32 AM   #5
rahulvarma
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Hi Andreas,

Actually i'm trying to predict the miRNA of Bombxy mori from the scaffold data aviable in mirbase database.The most preferable software for predicting mirna struc is ViennaRNA
Also i realize that RNALfold/RNAplfold are the preferable modules when we use large (genome)sequence. I Choose RNAplfold where i can choose window size.

RNAplfold [-L 70] [-W 70] [-T 37] [-4] [-noLP] [-noGU] [-noCloseGU] [-d2] [-c 0.001] <B-mori-genome.seq> B-mori-genome

when i run thr above program i get scaffold_ds.ps but not the secondary structure files.I.e. Dot plots something like ..(((((((..(........)...))))))).. this.

Could you please help me by giving the proper command line for predicting the structure if RNA from the B.mori genome using the module called RNAplfold with its sliding window size of 70nt.


Thanks in advance.
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Old 09-06-2011, 03:42 AM   #6
me_myself_andI
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Hi Raja,

can't check this right now, but as far as I remember RNAPlfold will not produce any other files than this postscript file. However, you can easily extract base pairing probabilities from that file. Just open it in a text editor - the format is described in there and I'm sure somewhere on the ViennaRNA website as well.

Andreas
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Old 09-06-2011, 09:23 PM   #7
rahulvarma
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Smile thank you

hi Andreas,

i was bit worried thinking about that may b am missing something in RNAplfold!ll look into text.

thank you very much for your timely hlep!
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Old 02-01-2013, 06:42 AM   #8
csmatyi
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How do you run RNAfold with a multifasta file producing multiple ps files, each with a sec structure file for each individual sequence? Plus, how do you print the energy values in the pdf?
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Old 07-21-2014, 03:48 PM   #9
delasa
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Default Free energy reported by RNAfold

What is the best way to interpret Free Energy for RNA-secondary structures reported by RNAfold?For example, what's the difference between free energy = -50 and free energy = -300?
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Old 07-21-2014, 05:37 PM   #10
me_myself_andI
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Delasa, no offense meant, but you should really do some background reading first. This is most basic (Bio)physics and needed to understand how any of this works.

Andreas
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Old 07-21-2014, 05:43 PM   #11
delasa
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I know what the free energies mean, I'm asking about interpretation of those energies in the biological context. I know my question is very basic and I apologize for that. Does the one with the lower energy have more probability to be degraded or not?
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Old 07-21-2014, 05:45 PM   #12
me_myself_andI
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In a nutshell: the one with more negative dG is more stable.

Andreas
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Old 07-21-2014, 06:02 PM   #13
delasa
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Thanks so much for you reply. Do highly or lowly structured transcripts differ in the free energies in their RNA secondary structures?
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Old 02-27-2016, 08:17 PM   #14
Sow
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Hi,
I'm trying to install ViennaRNA package on on home directory with the comman-
./configure --prefix/home/username
However after this the make command does not work:
***No targets specified and no makefile found.

could anyone tell me how can I install the ViennaRNA package in my home directory?

Thanks
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Old 02-28-2016, 03:10 AM   #15
mastal
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You should probably have a space between '--prefix' and '/home/username'.
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Old 02-28-2016, 08:20 AM   #16
Sow
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Thanks.
Yes I tried that but that doesn't even run the configure step.
Both make and make install steps do not work.
And I do see a make file in the ViennaRNA package.
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Old 02-28-2016, 01:46 PM   #17
mastal
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Actually, according to the manual,

http://www.tbi.univie.ac.at/RNA/docu...n.html#install

the correct syntax is:

./configure --prefix=/home/username/ViennaRNA


What type of computer/operating system are you trying to install the software on?

If make doen't work, have you tried downloading the precompiled binaries, if there are precompiled binaries for your system?
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