#!/usr/bin/perl -w use File::Spec; use CGI; use POSIX; $cgi = new CGI; print $cgi->header(); $cgi->start_html(-title=>'Scan for Motifs inputs'); ######################################################################################################## ################################### START SESSION ID ############################################## $time = localtime(time); # $time1 =time; $time =~ s/\s/_/g; $time =~ s/:/./g; $idnumber = $time; $idnumber .= "_"; for (my $i = 0; $i < 5; $i++) { $idnumber .= int (rand 10); } ################################## END SESSION ID ################################################# my $client_ip = $ENV{'REMOTE_ADDR'}; my $client_proxy=$ENV{'HTTP_X_FORWARDED_FOR'}; my $referrer=$ENV{'HTTP_REFERER'}; my $contents = $ENV{'QUERY_STRING'}; if(not defined $client_proxy){$client_proxy=$client_ip;} if(not defined $referrer or $referrer!~/otago\.ac\.nz/) { system("echo '$client_proxy from $client_ip \t$time \t No referrer, Terminated.\t $contents' >>/PROJECTS/ACCESS_DETAILS_OF_ALL_PROJECTS/ACCESS_DETAILS.txt"); exit; } #my $l_time=localtime(time); #open(APP,">>/PROJECTS/ACCESS_DETAILS_OF_ALL_PROJECTS/ACCESS_DETAILS.txt"); #flock(APP,2); #print APP "$client_proxy from $client_ip \tSFM \t$referrer\t TIME=$l_time\n"; #close(APP); ########################################################## ############# create a log file $log_file=$idnumber."_LOG.LOG"; open(WR_LOG,">tmp/$log_file") or print "$!"; print WR_LOG "OK\n"; close(WR_LOG); system("chmod 777 tmp/$log_file"); ############################## ########################################################## #exit; print qq~ Scan for Motifs input
1. Enter human a gene symbol to fetch a 3'UTR alignment (e.g. "TNF") :
 
 
OR
Search your own sequence or alignment for regulatory elements :
[ The following three formats are supported:
 
 
 
 
OR
Upload file containing the sequence in FASTA/multiFASTA/tabular MSA/ClustalW alignment format : 

2. Select one or more typers of translational control elements from the following:
A.  Automatically select all regulatory elements with an E-value <= per thousand bases from TransTerm. 
~; my $skip_1=0; if($skip_1==1) { ################################# query lancelot database use DBI; $host="localhost"; $db="tt2011"; $user="Ambarish"; $pwd="biswas1"; $connectionInfo="dbi:mysql:$db;$host"; # make connection to database $dbh = DBI->connect($connectionInfo,$user,$pwd); $cmd_select="select * from Signal order by Name"; $sth = $dbh->prepare($cmd_select); $sth->execute(); while(@row=$sth->fetchrow_array()) { #print "$row[0] $row[1]
"; for($i=0;$i<=$#row;$i++) { if(not defined $row[$i]) { $row[$i]="NA"; } } $signalid=$row[0];chomp $signalid; $publish=$row[1]; chomp $publish; $identifier=$row[2]; chomp $identifier;if(($identifier eq "") or ($identifier eq "NA")){next;} $dbid=$row[3]; chomp $dbid; $db_key=$row[4]; chomp $db_key; $pattern=$row[5]; chomp $pattern; $patsearch=$row[6]; chomp $patsearch; $rnamotifpattern=$row[7]; chomp $rnamotifpattern; $matrix=$row[8]; chomp $matrix; $description=$row[9]; chomp $description; $rfam=$row[10]; chomp $rfam; $utrdb=$row[11]; chomp $utrdb; $speciesdiscovered=$row[12]; chomp $speciesdiscovered; $species=$row[13]; chomp $species; $falsepositive=$row[14]; chomp $falsepositive; #$falsepositive=lc($falsepositive); $humanhit=$row[15]; chomp $humanhit; $fiveutr=$row[16]; chomp $fiveutr; $cds=$row[17]; chomp $cds; $threeutr=$row[18]; chomp $threeutr; $datemodified=$row[19]; chomp $datemodified; $modified_identifier=$identifier; $modified_identifier=~ s/\s+/_/g; if((not $publish eq "no") and (not $species eq "Prok") and (not $threeutr eq "No")) { #print "$identifier\t$species\t$threeutr\n"; if($falsepositive!~/NA/ and $falsepositive < 0.175) { print qq~
$identifier
~; print qq~

$identifier

Pattern : $pattern
$description
~; } else{ print qq~
$identifier
~; print qq~

$identifier

Pattern : $pattern
$description
~; } } } $sth->finish() or print "$!"; $dbh->disconnect() or print "$!"; } ########################################################################### print qq~
 Give your own pattern below : 
Examples:
r1={au,ua,gc,cg,gu,ug,ga,ag} p1=2...3 0...4 p2=2...5 1...5 r1\~p2 0...4 \~p1
^N CCCCC[1,1,1] 0...5 CCCC[1,0,0]

B.  Show those protein binding sites from RBPDB for which frequency matrices are available with an E-value <=  
C.  Show targets of conserved microRNA families as predicted by Targetscan 
D.  Show all base seed sequence targets from human microRNA's (miRBase) 
E.  Show elements not found in the reference sequence. 
 
~;