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I have been using the NCBI's BLAST stand-alone program to interrogate in-house transcriptome assemblies of different insect species. Using tBLASTx, I can often find matches between a given gene from Drosophila and a region of the interrogated insect transcriptome assembly.
My question is how to use tBLASTx to interrogate genomic DNA assemblies (with introns). Are there specific parameter settings (e.g., -G and -E) within tBLASTx that anyone has found useful or are there other more appropriate tools?
The software guides and associated materials have thus far been unhelpful for this question, but perhaps this answer will become apparent shortly.
My question is how to use tBLASTx to interrogate genomic DNA assemblies (with introns). Are there specific parameter settings (e.g., -G and -E) within tBLASTx that anyone has found useful or are there other more appropriate tools?
The software guides and associated materials have thus far been unhelpful for this question, but perhaps this answer will become apparent shortly.