Short sequence tissue specific BLAST - (Jan/15/2013 )
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!
I would select all transcripts known to be expressed in cardiac tissue first and somehow compile them up to the form of Entrez query and use it to limit the search.
As for the algorithm, I don't know much about the background theory of BLAST, but since I assume you expect only 100% match, you can probably increase the penalty for missmatches to limit it further. But that's just an idea.