Hello,
I apologize in advance if this question is trivial, I'm very new at all this.
I'm trying to do gene comparisons between two strains of bacteria, A and B. When I find a gene in A that doesn't blast to anything in B, I blast A against itself to see whether it's actually a small fragment of a larger gene. This is where I run into problems. When there's signficant overlap, I'm not sure how to decide whether the gene is actually unique in the operon, although small, or part of the gene downstream.
For example (for simplicity, although overlap is usually much more signifcant).
A, operon 1 gene 1 ATG/GCA/TGC/GCT/AGG/CCT/TGT/TCC/T....
A, operon 1 gene 2 ...AT/GGC/ATG/CGC/TAG
I know these two genes aren't in the same reading frame, but it is possible that two genes within the same operon have relateively signficant overlap but are still unique?
Any thoughts/ suggestions?
Thanks for taking time to read/comment.
