What is the fastest nucleotide sequence alignment search tool for 100mer queries versus a 2G database for nearly similar matches

Question

[a615ebfb]

Hello,

(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!

[cmdcolin]

are you aligning e.g. 100bp reads against a 2Gbp genome or something else? describing what type of sequence the db is and what type of sequence the queries are could help

[GenoMax]

I have tried blastn (megablast), blat, and mrfast.

Why are you looking for something else? What did blat not work for you? blat is the perfect and fast tool for the very application you note.

looking for nearly similar sequences > 90% identity.

There is no tool simpler than blat for searching multi-fasta sequences in files against each other without needing to create indexes etc. It works both with protein and DNA sequence.

Answer 1

[cfos4698]

diamond is very fast:

Here, we introduce a greatly improved version of DIAMOND that provides two sensitivity modes, --very-sensitive and --ultra-sensitive, which will enable data-intensive comparative genomics research such as tree-of-life scale tracing of protein evolution5, gene age inference6,7, and functional annotation of genes and gene families8 to be carried out with the same accuracy as BLAST, but with an 80–360-fold computational speedup. In --ultra-sensitive mode, DIAMOND (v2.0.7) achieves this BLAST-like sensitivity milestone while reducing the computational run time of BLASTP-heavy studies from months to hours.

the paper