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Hey,
I'm looking at a short motif sequence of 8 bases and I would like to find all genes and transscripts with this sequence in cardiac tissue. I tried blasting, but the short sequence seems to cloud results or I'm not supplying the correct parameters to the algorithm. I managed to get some hits from refseq RNA after playing with the "expected" and "word" settings, but surprisingly the transscript which the sequence is actually in (ubiquitin) was nowhere to be found, so I'm pretty sure I didn't get all the results (even though my max results were set at 20.000). For the tissue specific part, I have no idea where to begin. Any ideas how to solve this problem would be greatly appreciated!
