Question: Blastx Against Swissprot
1
gravatar for User 1330
8.3 years ago by
User 133060
User 133060 wrote:

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 • 2.4k views
ADD COMMENTlink modified 3.5 years ago by Biostar ♦♦ 20 • written 8.3 years ago by User 133060
2

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 REPLYlink written 8.3 years ago by Timtico330
4
gravatar for Pierre Lindenbaum
8.3 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum119k wrote:

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

ADD COMMENTlink written 8.3 years ago by Pierre Lindenbaum119k

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

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by 5heikki8.4k
0
gravatar for Larry_Parnell
7.7 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

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.

ADD COMMENTlink written 7.7 years ago by Larry_Parnell16k
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