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  • Can I BLAST/BLAT a subregion of the genome?

    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.

  • #2
    I just tried a 33 mer and got results back with blat against human genome. You can provide sequence of a single chromosome to restrict your search for that specific chromosome (or even a region).

    Have you tried to use bowtie1, bbmap or a similar NGS aligner?

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