I'm trying to find iterations of (or close matches to) a 35bp sequence. BLAT is not helpful as there are too many iterations of the sequence in the human genome for it to deal with*.
Is there a way I can BLAT/BLAST/similar for matches to a query sequence just in a subset of the human genome, e.g. a single chromosome?
*I'm assuming this is the problem. I get the error 'no matches found' but I have often got this in the past when the problem was, in fact, that too many matches existed.
Is there a way I can BLAT/BLAST/similar for matches to a query sequence just in a subset of the human genome, e.g. a single chromosome?
*I'm assuming this is the problem. I get the error 'no matches found' but I have often got this in the past when the problem was, in fact, that too many matches existed.
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