I am interested in running a blastn search to search for complementary sequence (potential biological function) between two groups of sequences, (Query blasted against Reference) such that the query is complementary to the minus strand of the reference. With blastall v. 2.2.14 installed on our server, I can't figure out how to display only the plus-minus results without the plus-plus results. Does anyone know of a way to get blast to run a nuc vs. nuc search and only report the results in the plus-minus strand orientation? If not, I will just have to parse out the results with perl.
Thank you very much.