I've noticed that the web-based and local BLAST homolog search in Prime give different results. Why is that?

The web server uses a different version of the BLAST executable. Schrödinger software should be compatible with the most recent BLAST version, but unfortunately not the new "blast+" series."

In our tests, after updating the BLAST database using $SCHRODINGER/utilities/update_BLASTDB, we do not see a big difference between web-based and local searches, We do see slight differences in the ranking of the homologs between the local and web-based search, but in general the same templates are found.

Keywords: Prime, homology modeling, homolog, BLAST

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