Rna Base Paring
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?
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.
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| 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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