Rna Base Paring

Question

[layal]

Is there any program that takes as an input two RNA sequences and tells you as an output which regions from both sequences possibly base-pair with each other? example:

S1: ACGGGCGUCGC

S2: AUCCCGCAAUA

Then the output will be GGGCGU from S1 and CCCGCA for S2. Also such segments in the output may not entirely basepair, allowing for some loops or hairpins.

[Biomonika (Noolean)]

I am not sure if you by "base-pair with each other" mean sequence alignment - then you could use for example one of many online tools (such as http://www.ebi.ac.uk/Tools/psa/emboss_water/nucleotide.html) or RNA folding - then you might want to google for RNA folding algorithms, such as http://mfold.rna.albany.edu/?q=mfold/RNA-Folding-Form

[layal]

Thanks, yet what I need is a program that tells me which parts of two input RNA sequences can possibly basepair with each other. I edited the question.

Answer 1

[Fabrice Jossinet]

what about DuplexFold? http://goo.gl/9i0WsV

[gauravdube007]

Hello Fabrice Jossinet, can you please help me with this post??

Can Anyone Suggest Me A Program For Converting Dot-Bracket Notation Format To Standard Hybridization Format.

Thanks in advance.

Answer 2

[Pierre Lindenbaum]

I found the match using ntdpal (part of the primer3 package)

$ primer3-2.3.5/src/ntdpal  -gval 5.0 -lval 5.0 -p ACGGGCGTCGC `echo -n "ATCCCGCAATA" | tr "ATGC" "TACG"` g
ACGGGCGTCGC                                                           
  ||||||                                                              
TAGGGCGTTAT                                                           
______________________________________________________________________
|ACGGGCGTCGC|  |TAGGGCGTTAT| g score=1.00 len=11 |0,0|1,1|2,2|3,3|4,4|5,5|6,6|7,7|8,8|9,9|10,10|