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Article ID: 1109 - Last Modified:

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

There is always a chance of differences between the web-based and local BLAST searches because of updates to the web database that are not (yet) included in your local BLAST installation. You can update your local database with the utility update_BLASTDB, as described in the Prime User Manual.

If you are using a software release earlier than 2014-4, you may notice differences because the web server uses BLAST+ but the local search with Schrödinger software uses BLAST. As of 2014-4, the local search also used BLAST+.

In our tests with an up-to-date BLAST database, 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: homology modeling

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