I did a local standalone blast pre-miRNAs against a genome in tabular format (-m 8) and got the results. Makembindex will index every stride-th N-mer of the database. This parameter is ignored if -legacy true is The makembindex command has a lot of options I'm not using - can I prune the large (~10+ GB) MegaBLAST index by choosing a different nmer? Or are there important tweaks to stride? The -task blastn command runs in ~ 2 hours, while the indexed (MegaBLAST) command runs in ~ 3 minutes. $ blastn -db hg18 -use_index true -query input.fa -evalue 1e-05 -num_descriptions 1 -num_alignments 1 -outfmt 6 $ blastn -task blastn -db hg18 -query input.fa -evalue 1e-05 -num_descriptions 1 -num_alignments 1 -outfmt 6 $ makembindex -input hg18 -output hg18 -iformat blastdb It's exponentially faster than normal blastn for this purpose, but I'm not sure what settings I should use when building MegaBLAST databases. I've been using MegaBLAST (in BLAST+) to test for high-similarity matches against hg18.
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