I'm trying to generate PSSM profiles from fasta files with PSI-BLAST and nr database, but it took around 10 minutes for 1 file. If I have many fasta files, it will take a lot of time.
So any suggestions for reducing the time or we have way to reduce nr database?
Thank you,
Khanh Le
Ahmet Sinan Yavuz
PSI-BLAST is an iterative tool and nr is a large database. So, it is expected to take some time. Reducing or changing the database may not be a suitable solution, depending on your use case for the generated PSSM file. However, in order to speed up the PSI-BLAST itself, you can reduce the number of iterations (-num_iterations parameter) and increase the number of threads to use all CPUs in your system (-num_threads parameter).
Good luck!
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