Question: Blast Against Swissprot Db
3
gravatar for Bdv
10.1 years ago by
Bdv310
Bdv310 wrote:

Hi I downloaded the swissprot database and used the command formatdb and then tried blastx against this database, I used the command: megablast -b 1 -T T -i....results.html I received results but with no links. When I blast against the nr or nt databases there are links there in the result file. What could be the reason for that? Thanks!!

uniprot blast • 5.4k views
ADD COMMENTlink modified 9.5 years ago by Anuraj Nayarisseri750 • written 10.1 years ago by Bdv310
1

But is it the right way to blast against the swissprot? to create the db with formatdb? so you suggest to use a script which adds the link? I need to parse the result html file to some table whith the hits and descriptions, to make it readeble...

ADD REPLYlink written 10.1 years ago by User 133060

please, comment after my answer, don't create a new thread.

ADD REPLYlink written 10.1 years ago by Pierre Lindenbaum133k

why do you use two accounts to connect on biostar ?

ADD REPLYlink written 10.1 years ago by Pierre Lindenbaum133k
4
gravatar for Pierre Lindenbaum
10.1 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum133k wrote:

It's because NCBI blast has been integrated with the Entrez database. Most sequences here have a unique number called gi linking to an unique record in the NCBI-Entrez Database.

When you're running your local BLAST, the engine doesn't know anything about the database that was created with formatdb, there is no meta-information.

In the case of swissprot, I guess the URL can be easily created from the FASTA header of each sequence because it should contain an accession number. e.g. the URL for Q04637 is http://www.uniprot.org/uniprot/Q04637

ADD COMMENTlink written 10.1 years ago by Pierre Lindenbaum133k
2
gravatar for Anuraj Nayarisseri
10.0 years ago by
Indore
Anuraj Nayarisseri750 wrote:

First you have to format your database following is the command for formatting

formatdb -i swissprot -p T -o T

Then you can perform blast

blastall -p megablast - d swissprot -i (here input your filename with extension) -o result.txt

this time it will create your result in result.txt file in bin folder.

Hope this will help you.

ADD COMMENTlink modified 16 months ago by _r_am32k • written 10.0 years ago by Anuraj Nayarisseri750
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