Rna Base Paring
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8.9 years ago
layal ▴ 10

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.

rna tool • 2.2k views
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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

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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.

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8.9 years ago

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

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8.9 years ago

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|
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