<input type=hidden name="var" value="test">
<input type=text name="var" value="test">
<select name="var">
    <option>test</option>
</select>

my $req = POST $URL, {var=>"value", selectvar=>"selectvalue"};
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Search Database: <select NAME="DATALIB">
<option VALUE="oasis_smart"> Smart v3.3 - 569 PSSMs
<option VALUE="oasis_pfam"> Pfam v6.6 - 3071 PSSMs
<option VALUE="oasis_sap" SELECTED> All - 3693 PSSMs
</select>
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#!/usr/bin/perl

use strict;
use HTTP::Request::Common qw(POST);
use LWP::UserAgent;

my $ua = LWP::UserAgent->new;

my $string = ">CG2B_MARGL\n ";
$string .= "MLNGENVDSRIMGKVATRASSKGVKSTLGTRGALENISNVARNNLQAGAK\n";
$string .= "KELVKAKRGMTKSKATSSLQSVMGLNVEPMEKAKPQSPEPMDMSEINSAL\n";
$string .= "EAFSQNLLEGVEDIDKNDFDNPQLCSEFVNDIYQYMRKLEREFKVRTDYM\n"; 
$string .= "TIQEITERMRSILIDWLVQVHLRFHLLQETLFLTIQILDRYLEVQPVSKN\n";
$string .= "KLQLVGVTSMLIAAKYEEMYPPEIGDFVYITDNAYTKAQIRSMECNILRR\n";
$string .= "LDFSLGKPLCIHFLRRNSKAGGVDGQKHTMAKYLMELTLPEYAFVPYDPS\n"; 
$string .= "EIAAAALCLSSKILEPDMEWGTTLVHYSAYSEDHLMPIVQKMALVLKNAP\n"; 
$string .= "TAKFQAVRKKYSSAKFMNVSTISALTSSTVMDLADQMC";


my $req=POST 'http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi',
   [ SEQUENCE=>"$string", 
     DATALIB=>'oasis_sap', 
     INPUT_TYPE=>'fasta', 
     EXPECT=>'0.01',
     FILTER=>'T', 
     SMODE=>'0', 
     NHITS=>'50', 
     GRAPH=>'2', 
     PAIR=>'2', 
     GW=>'-1'];


 print "Content-type: text/html\n\n";
 print $ua->request($req)->as_string();
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A little bit off-topic, but your setting of $string is rather laboriuos. Wouldn't it be much easier to use a HERE document, like so:

my $string=<<EOSTRING;
CG2B_MARGL
MLNGENVDSRIMGKVATRASSKGVKSTLGTRGALENISNVARNNLQAGAK
...
TAKFQAVRKKYSSAKFMNVSTISALTSSTVMDLADQMC
EOSTRING
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?

$request = GET
           'http://jobsearch.monster.com/jobsearch.asp',
       [
         ah=>'http://jobsearch.monster.com/',
         pg=>'1',
         cq=>$query,
         col=>'dltci',
         mx=>'1000',
         pp=>'500',
         lid=> '354',
         cy=>'US',
         st=>'CA',
         brd=>'1'
         
        ];

  $response = $ua->request($request);

  $r = $response->as_string;
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Scott

Thanks guys for the response...it seems so obvious now...can't believe I couldn't figure it out
No worries Scott, I plan to use this program as a model for many other things besides NCBI.
I am now having another problem that I had working before...I am trying to loop in many individual pieces of text...one at a time, after receiving the response from the server. Here is the code that worked before in a simple manner...


#!/usr/bin/perl 

use lib "/System/Library/Perl";
use HTTP::Request::Common qw(POST);
use LWP::UserAgent;

$ua = LWP::UserAgent->new();

print "Which file do you wish to process?\n";
chomp($file=<STDIN>);
open (FILE, "$file") || die "$!";

print "Please enter name for the output file\n";
chomp($out=<STDIN>);
open (OUT, ">$out") || die "$!";

while (<FILE>) {        
@acc = <FILE>;
}
print "\nPROCESSING file $file...\n";

for ($i=0;$i<=$#acc;$i++) {
$accession = $acc[$i];
chomp $accession;
etc....I have made the necessary corrections now
[download]

I continue to get an error from the server and I only have one sequence in the input file.
Any thoughts??
Thanks again guys!
Dr.J

Well, I am not sure of the exact nature of your problem from you description, but I would clean up a few stylistic things, and maybe along the way your problem will clear up too.

First, when reading in a file you can either do it in a while loop, in which case it will read in line by line, or you can slurp it all at once by assigning the filehandle to an array (each line becoming an element of the array). You've done a hybrid of both here, and that may be the source of your problem. Most people agree that the way to go is to read line by line, that way if you get an input file that is bigger than you expect, you don't pay any penalties for slurping a huge file into memory.

Also, since you are reading the file in line by line, you can do the rest of the work in the while loop, resulting in:

print "\nPROCESSING file $file...\n";
while (<FILE>) {        
   chomp $_;
   $accession = $_;
   etc....I have made the necessary corrections now
}
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If you desided you don't want to do it that way, I would at least change your for loop to a more Perlish loop:

foreach my $accession(@acc) {
    chomp $accession;
    etc....I have made the necessary corrections now
}
[download]

Good luck,
Scott