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.
what about DuplexFold? http://goo.gl/9i0WsV
Hello Fabrice Jossinet, can you please help me with this post??
Thanks in advance.
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gauravdube007 •
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
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TAGGGCGTTAT
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|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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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
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.