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!!
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
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.