makeblastdb performance benchmark
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10 weeks ago
drquestion ▴ 20

Hello everyone!

Recently I've had to allocate some resources to build a blast database, but then I realized I had no idea of how many I had to give.

Doing some research around I didn't find anything answering my question: has anyone ever done some benchmarking on runtime and memory consumption for makeblastdb? For example, given n input sequences, what is the complexity of the complete set of computations made by makeblastdb?

makeblastdb performance runtime memory blast • 232 views
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Someone may have a more analytical answer, but in my experience this is something you need not worry about. For a large database - no quite nr but maybe 3-4x smaller - the index database will be created in a matter of minutes. So it may be closer to an hour for nr, but I don't think you need to prepare for it other than having a good amount of memory and disk space.

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Thank you very much, it took around one hour and a half for the whole UniProt sequences database, indeed!

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