Question

Blastx Against Swissprot

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13.9 years ago

User 1330 ▴ 60

Hi

I want to blastx a huge sequnce set against swissprot (as it takes too long aginst nr), is it possible in a resonable time with a regular hardware and how to install and run it locally?

Thanks alot!

blast uniprot hardware • 4.3k views

ADD COMMENT • link updated 9.1 years ago by Biostar 20 • written 13.9 years ago by User 1330 ▴ 60

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your question is way too broad.. "how to install and run it"??? google, download, try and after that ask. +1 to Pierre Lindenbaum for the link.

ADD REPLY • link 13.9 years ago by Timtico ▴ 330

score 4 · Answer 1 · 2010-12-21

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13.9 years ago

Pierre Lindenbaum 164k

Blast can be downloaded from the NCBI and swissprot from www.uniprot.org .

ADD COMMENT • link 13.9 years ago by Pierre Lindenbaum 164k

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The last major update is also available through the NCBI: swissprot.tar.gz | Swiss-Prot sequence database (last major update).

ADD REPLY • link 9.1 years ago by 5heikki 11k

score 0 · Answer 2 · 2011-08-26

Yes, it is possible "in a resonable time with a regular hardware." Use the links Pierre gave and run 100 or 1000 searches. See how long those take and then look for ways to optimize the process if need be. Each compute environment is different and so it is difficult to say with absolute certainty how long a job will take until one tries a subset of the queries.