Question: Dna Secondary Structure Prediction Of A Large Dataset
2
gravatar for Timtico
7.5 years ago by
Timtico330
NL
Timtico330 wrote:

Hi,

I'm interested in prediction of hairpin structures from a large set of DNA sequences (fasta), which I extracted using my own perl scripts.

I'm looking for a tool that creates predictions of secondary structure (e.g. hairpin loops), and gives me some basic information such as free energy.

output should preferably in dot.bracket FASTA fileformat, so I can easily visualize the structures with known tools.

My weapons of choice would be either Perl or R. (I'm struggling with Taverna)

thanks in advance!

perl R dna secondary • 8.4k views
ADD COMMENTlink modified 7.5 years ago • written 7.5 years ago by Timtico330
1

DNA ? not RNA ?

ADD REPLYlink written 7.5 years ago by Pierre Lindenbaum115k

yeah indeed DNA

ADD REPLYlink written 7.5 years ago by Timtico330

DNA secondary structure should be an ideal double strand, there isn't much to predict?! I assume you are looking for potential transcripts (haipin sounds like miRNA) by scanning genomic sequence.

ADD REPLYlink written 7.5 years ago by Cjt370

think single-stranded DNA.

ADD REPLYlink written 7.5 years ago by Aaronquinlan10k

No i'm looking for specific hairpins surrounding a consensus sequence, indeed: think single stranded.

ADD REPLYlink written 7.5 years ago by Timtico330

indeed, think single stranded.

ADD REPLYlink written 7.5 years ago by Timtico330
5
gravatar for Pasta
7.5 years ago by
Pasta1.3k
Switzerland
Pasta1.3k wrote:

I would use RNAfold from the Vienna RNA package which works for DNA too : http://rna.tbi.univie.ac.at/. You can either call the program from Perl or make a Perl version of the available source code.

As far as I can remember, you just supply a FASTA file and you will get dG and other thermodynamic values for each of your sequences.

ADD COMMENTlink modified 7.5 years ago • written 7.5 years ago by Pasta1.3k

Thanks, I took a look at the code but i'm not very proficient in C. I found Unafold however, It's Perl based. I will try to make it work but running into some troubles.

ADD REPLYlink written 7.5 years ago by Timtico330
2
gravatar for Asaf
7.5 years ago by
Asaf5.0k
Israel
Asaf5.0k wrote:

Try using RNAplfold from the same package, it predicts stable local structures that you can obtain from the dot-plot or use the -u option to get the probability for a region being unpaired. You can run the program and then use perl to digest the output

ADD COMMENTlink written 7.5 years ago by Asaf5.0k
1
gravatar for Sequencegeek
7.5 years ago by
Sequencegeek740
UCLA
Sequencegeek740 wrote:

Hi There,

If you are interested in more detailed information about the hairpin, there is a script on this page that will parse the RNAFold output. It may be a little buggy but it has worked for me in the past. RNA fold Topic

ADD COMMENTlink written 7.5 years ago by Sequencegeek740
1
gravatar for Timtico
7.5 years ago by
Timtico330
NL
Timtico330 wrote:

I ended up writing a wrapper/parser in Perl for the commandline executed RNAstructure package (University of Rochester) althought it's abit of a hack it works really well for my purposes.

The script takes a multiple sequence FASTA file and processes each sequence with fold.exe of the package. The results are gathered in dot.bracket FASTA file. From this, postscript images are created, depicting the predicted structure(s). Cutoff can be manually set to obtain only the structures with the highest likelyhood. All postscript files are gathered and output is combined into a single PDF-file using Ghostscript.

ADD COMMENTlink modified 6.8 years ago • written 7.5 years ago by Timtico330
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