I need a tool that must be faster, but not necessarily as sensitive, than BLAST in searches of DNA sequence against a DNA database. I know some tools such as Diamond, which is much faster than BLASTx and BLASTp, but it doesn't work for BLASTn-like situations. I already have tried USEARCH, but only its 32-bit version is available for free, and can only deal with small/medium datasets.
BLAT:
https://en.wikipedia.org/wiki/BLAT_(bioinformatics)
http://genome.cshlp.org/content/12/4/656.full
You can try to use local BLAST, or maybe a perl or python script. Another option could be Hmmer: http://hmmer.org/.
However, I think BLAST it is your best option.
BLAT:
https://en.wikipedia.org/wiki/BLAT_(bioinformatics)
http://genome.cshlp.org/content/12/4/656.full
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