How to generate Links in WWW BLAST server ??

Simon Andrews simon.andrews at bbsrc.ac.uk
Tue Nov 27 04:48:21 EST 2001


Ingo Klein wrote:
> 
> Hi yall,
> I'm setting up a WWW BLAST server for a friend.
> The Searchengine is up and running happy.
> 
> The only problem is :
> 
> If I search a sequence in the NCBI-Test database, I get links for
> further information about the found sequence. If I do the same with
> our generated database, these links are missing...
> 
> Any Help,Links,Sources or what ever whould be nice...


Funny you should ask - I'm just doing this myself!  In our case I have a
subroutine in the blast CGI script which monitors the blast output
stream and looks for a particular pattern (whatever describes the
sequence identifiers in your database).  Where it finds a sequence name,
it substitutes it for a link containing the same text, with a hyperlink
to another CGI script to get more info.

In our case, the link is to another internal script, but you could link
out to NCBI or whatever you want.

I don't know what language you're using to write your CGI in, but in
Perl the relevant bit of our script looks like (this isn't exact and is
untested, but should give you an idea);

while (<PIPEOUTOFBLAST>) {

	if (/Pattern_for_seq_name/){

		s#(Pattern_for_seq_name)#<a href="http://whaterer.link?id=$1>$1</a>#;
	}	

	print;
}

This assumes that you are running blastall with the -T option, so you
are generating HTML anyway.

Hope this helps

Simon.




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