Find Sense Antisense Pairs In 2 Fasta Files

Question

[jkhurana2311]

I have done some small RNA mapping to my genome of interest. Then, I extracted fasta sequence from two bed files mapping to the plus and minus strand of the genome. I am interested in searching for sense antisense pairs in those fasta files to see if some of those sequences would be complementary to each other. Is there a set of tools which would allow me to do that. I have reasonable unix experience but lack in programming.

Thanks

[Eric Normandeau]

Are you looking for 100% identity or accepting differences? In both cases, blasts may give you what you want fast. Blast your group of sequences on itself, keep only pairs of sequences that have high or perfect identity, and have opposite sense.