#!/usr/local/bin/perl $ENV{'PERL5LIB'}="/usr/local/lib/perl5"; $ENV{'PGPLOT_BACKGROUND'}="white"; $ENV{'PGPLOT_FOREGROUND'}="black"; #require ("/usr/local/lib/perl5/pgplot.pl"); &primeRegSubs; if ($ARGV[0]=~/-gtest/) { # &blastGraph($ARGV[1],"/XWIN"); exit; } $queryString = $ENV{'QUERY_STRING'}; if ( $queryString=~/^gif=on/i) { $gifOn=1; } else { $gifOn=0 ; } $queryString=~s/^gif=[a-z]+\&//; if ( $queryString =~ m/sequence/) { &doblast; } else { &intro; } exit; sub doblast { &printHeader("BLASTN Results"); $queryString =~ s/%3E/>/g; $queryString =~ s/%0A/\n/g; $queryString =~ s/%0D/ /g; $queryString =~ s/^sequence=//g; $queryString =~ s/[+]/ /g; $database = "$dpiDocsPath/sites.fasta"; $blastFile=&genSeqFile($queryString); $command="dec_blast/blastall -pblastn -b0 -ddec_blast/sites.fasta -i$blastFile -o$blastFile.out\n"; #print "Executing $command\n"; system($command); #`touch /tmp/index.html; dec_blast/blastall -pblastn -b0 -ddec_blast/sites.fasta -i$blastFile -o$blastFile.out`; ; if ($gifOn==1) { # &blastGraph("$blastFile.out","$blastFile.gif/GIF"); print "\n"; print "
Blue: forward strand. Red: complementary strand.
\n";
}
open(BLAST,"$blastFile.out");
while ( $_ =
Note: This database copyright 1994 Harvard University.
Robison, K., and Church, G.M. DPInteract: A database on DNA-protein interactions. (1994). Electronically published and manuscript in preparation.
Please contact $mailKr to report additional data or problems with this database."; }
elsif (m/^Sequences producing/) {}
# { print "
Enter a DNA sequence with either no comments or in FASTA format. You may include spaces and carriage returns in the sequence entry; they will be ignored by BLAST.
\n\n\t\t+ Proven site\t? Candidate site\t- Pseudo-site\n"; }
elsif (m/^Query=/) { print "
$_"; }
elsif (m/^Database:/) { print "
Database: Ec DNA BP Ds:\t+ Proven\t? Candidate\t- Pseudo\n"; }
else
{
s!^([+\-\?])([a-zA-Z0-9_]*)([ \t]*#)([0-9]*)!$1$2$3$4!o;
s!^>(.)([a-zA-Z0-9_]*)([ \t]*#)([0-9]*)!>$1$2$3$4!o;
print $_;
}
}
}
print "
$claimer";
if (rand(10)<1) { &cleanup; }
exit;
}
sub intro
{
&printHeader("BLASTN Search");
print '
Please report problems with this service to krobison@nucleus.harvard.edu
';
exit;
}
sub blastGraph
{
local($blastData,$outDevice)=@_;
local($i);
open(BLAST,$blastData);
while ( $_ = $title
\n";
}
sub primeRegSubs
{
$RelayBase = "http://golgi.harvard.edu/htbin/relay";
$Cgsc = "http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/";
$GenbankA = "$RelayBase/genbank-acc?";
$Medline = "http://golgi.harvard.edu/htbin/dpinteract/medline-muid?";
$MedNeigh = 'http://atlas.nlm.nih.gov:5700/htbin/enf/entrezmmnei?';
$Pir = "http://www3.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=p&form=6&uid=";
$Pdb = 'http://expasy.hcuge.ch/cgi-bin/pdb_entry_or_image?';
$Prints = 'http://www.biochem.ucl.ac.uk/cgi-bin/attwood/DoPRINTS.pl?cmd_a=Display&qua_a=/Full&fun_a=Code&qst_a=';
$Blocks = 'http://www.blocks.fhcrc.org/blocks-bin/getblock.www?';
$dpiServer = "http://arep.med.harvard.edu";
$dpiCgi = "$dpiServer/cgi-bin/dpinteract";
$dpiDocsPath = "/usr/arep/a3/httpd/htdocs/dpinteract";
$dpiDocsUrl ="$dpiServer/dpinteract";
$dpiFam = "$dpiCgi/family?";
$dpiSfam = "$dpiCgi/subfamily?";
$dpiGene = "$dpiCgi/gene?";
$dpiClass = "$dpiCgi/class?";
$dpiMsearch = "$dpiCgi/msearch?";
$dpiSearch = "$dpiCgi/search?";
$dpiRefSearch = "$dpiCgi/ref?";
$dpiMrefSearch = "$dpiCgi/mref?";
$dpiSeqregSearch = "$dpiCgi/seqreg?";
$dpiBlastnSearch = "$dpiCgi/blastn";
$dpiMatSearch = "$dpiCgi/matsrch";
$Expasy = "http://expasy.hcuge.ch";
$Prosite = "$Expasy/cgi-bin/get-prosite-entry?";
$Prodoc = "$Expasy/cgi-bin/get-prodoc-entry?";
$Scop = "http://www.bio.cam.ac.uk/scop/data";
# $Sprot = "$Expasy/cgi-bin/get-sprot-entry?";
$Sprot = "http://expasy.hcuge.ch/cgi-bin/get-sprot-entry?";
$SprotPi = "http://expasy.hcuge.ch/cgi-bin/getpI?";
$seqAnalRef = "$Expasy/cgi-bin/get-seqanalr-entry?";
$ecocycGene="http://ecocyc.ai.sri.com:1555/new-image?type=GENE&object=EG";
$ecocycMap="http://ecocyc.ai.sri.com:1555/new-image?type=LOCUS-POSITION&object=EG";
$entrezProtein = "http://www3.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=p&form=6&Dopt=r&uid=";
$entrezMedline = "http://www3.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=m&form=6&Dopt=r&uid=";
$mailKr = 'krobison@nucleus.harvard.edu';
$claimer = "
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