(1) What is the fastest nucleotide versus nucleotide sequence search method that I can install locally for doing searches?
(2) Are there any publications to support this?
(3) Do you have benchmarked results or can point me to any?
My application: 100mer nucleotide queries versus a 2G nucleotide database. I am not looking for remote homologs but am looking for nearly similar sequences > 90% identity. Multithreaded would be great but I can also run in parallel. So, either option is good.
I have tried blastn (megablast), blat, and mrfast. Thanks!