QTL Viewer

"; } else { echo ""; } echo ""; } } if ($sp2=="----none----") break; } echo "

Select source species:	Select intermediate species:	Select target species:	Select Metatrait (Disease):

Gap tolerance: "; ?>	Avg. id. Species 1 -> 2: "; ?>	Avg. id. Species 1+ 2 -> 3: "; ?>	Fix borders on centroid "; else echo ">"; ?>

Please select properties from above selection. [HELP]

\n"; if (empty($sp1) || empty($sp2) || empty($sp3) || $sp1==$sp2 || $sp1==$sp3 || $sp2==$sp3) { echo "

"; echo "Back to qtl.pzr.uni-rostock.de"; echo ", for feedback or assistance please contact Pablo Serrano-Fernández or Steffen Möller\n"; exit; } if (empty($tol) || $tol<1000 || $tol>500000){ $tol=10000; } if (empty($metatrait)) $metatrait="EAE/MS"; if (empty($afn) || $afn<50 || $afn>100){ echo "

Minimal similarity between first and second species was not properly set ('$afn'), setting it to 90

\n"; $afn=90; } if (empty($afn2) || $afn2<50 || $afn2>100){ echo "

Minimal similarity between consensi of first and second species to the third was not properly set ('$afn2'), setting it to 60

\n"; $afn2=60; } $start_qtl=array(); $stop_qtl=array(); $n=array(); $a=array(); $chr=array(); $joined=array(); $sp2LinkToExpressionview=array(); $sp3LinkToExpressionview=array(); $metatrait=strtolower(substr($metatrait,0,3)); for ($i=1; $i<20; $i++) { array_push ($chr,$i); } array_push ($chr, 'X'); $match=array(); //$connect=mysql_connect("kaka.sanger.ac.uk","anonymous",""); # Use this for direct connection to ensembl.org $connect=mysql_connect("rack8.pzr.uni-rostock.de","correlation","",TRUE); if (!$connect) { echo "Could not connect to MySQL server."; exit; } if (!mysql_select_db("ensembl_compara_16_1",$connect)) { echo "Could not select database on server."; mysql_close($connect); exit; } $connectQTL=mysql_connect("rack8.pzr.uni-rostock.de","correlation","",TRUE); # now (6.4.2004) in rack8 if (!$connectQTL) { echo "

Could not connect to MySQL server.

"; mysql_close($connect); exit; } ######################################################### FUNCTIONS ################################################################### #######################-------- Get QTLs ---------####################### function getqtls ($db,$trait,$sp) { global $start_qtl; global $stop_qtl; global $connectQTL; global $centroid; global $metatrait; $tmp=0; if ($centroid=="on"){ if ($sp=="Homo_sapiens") $query="SELECT chr,start_centroid,stop_centroid,name,start_mrk FROM ".$metatrait."_qtl WHERE species='$sp' "; else $query="SELECT chr,start_centroid,stop_centroid,name FROM ".$metatrait."_qtl WHERE species='$sp' "; } else { if ($sp=="Homo_sapiens") $query="SELECT chr,start_bps,stop_bps,name,start_mrk FROM ".$metatrait."_qtl WHERE species='$sp' "; else $query="SELECT chr,start_bps,stop_bps,name FROM ".$metatrait."_qtl WHERE species='$sp' "; } if (!empty($trait)) $query .= " AND trait='$trait'"; $query .= " order by 1,2,3"; if (!mysql_select_db($db,$connectQTL)) { echo "Could not select database on server."; mysql_close($connect); mysql_close($connectQTL); exit; } $result=mysql_query($query,$connectQTL); if (!$result) { echo "Could not execute query '$query'"; mysql_close($connect); mysql_close($connectQTL); exit; } $ret=array(); for ($i=0; $n=mysql_fetch_row($result); $i++) { if ($n[1]>$n[2]) { $tmp=$n[1]; $n[1]=$n[2]; $n[2]=$tmp; } $ret[]=$n; } mysql_free_result ($result); return $ret; } #######################-------- Orgname 2 Genomedbid ---------####################### function orgname2genomedbid($org) { $org=str_replace("_"," ",$org); $org=strtolower($org); switch($org) { case "homo sapiens": case "human": return 1; break; case "mus musculus": case "mouse": return 2; break; case "rattus norvegicus": case "rat": return 3; break; default: return $org; } } #######################-------- Get Frags ---------####################### function getfrags ($c,$begin,$end,$orgQTL,$orgFrag,$affn) { global $connect; $query="SELECT consensusfrag.name, consensus_start, consensus_end, perc_id FROM dnafrag AS consensusfrag, genomic_align_block AS gab, dnafrag AS queryfrag WHERE consensusfrag.dnafrag_id = gab.consensus_dnafrag_id AND queryfrag.dnafrag_id = gab.query_dnafrag_id AND ( (query_start > $begin AND query_start < $end) OR (query_end > $begin AND query_end < $end) ) AND queryfrag.name='$c' AND queryfrag.genome_db_id=".orgname2genomedbid($orgQTL)." AND consensusfrag.genome_db_id=".orgname2genomedbid($orgFrag); if ($affn>=0) { $query .= " AND perc_id>$affn "; } $query .= " ORDER BY consensusfrag.name,consensus_start"; $result=mysql_query($query,$connect); if (mysql_errno($connect)) { echo "

Could not execute query '$query' because of error '".mysql_error($connect)."'

"; mysql_close($connect); mysql_close($connectQTL); exit; } $ret=array(); for ($i=0; $n=mysql_fetch_row($result); $i++) { $ret[]=$n; } mysql_free_result ($result); return $ret; } #######################-------- Fragment matching QTLs ---------####################### function fragmatchqtl($chr,$s,$e,$qtlsp) { $ret=array(); $resulthistory=array(); foreach ($qtlsp as $i) { $ret[0]=0; $ret[1]=0; $ret[2]=0; if($chr==$i[0]){ $ret[1]=$i[1]; $ret[2]=$i[2]; if ($s>=$i[1] && $s<=$i[2]) { $ret[0]=1; $ret[1]=$s; } if ($e>=$i[1] && $e<=$i[2]) { $ret[0]=1; $ret[2]=$e; } if ($s<=$i[1] && $e>=$i[2]) { $ret[0]=1; } if (1 == $ret[0]) { array_push($resulthistory,array("chr"=>$chr, "s"=>$ret[1], "e"=>$ret[2], "n"=>$i[3], "mrk"=>$i[4])); } } } return $resulthistory; } #######################-------- Join Fragments ---------####################### function joinfrags ($frags,$qtlsp) { $c=0; $s=0; $e=0; $min_perc_id=100; $sum_perc_id=0; $subfrags=0; $match=array(); global $tol; $reshis=array(); foreach($frags as $f) { if (0==$c) { // init, first record special case $subfrags++; $c=$f[0]; $s=$f[1]; $e=$f[2]; if (count($f)>=4) { $min_perc_id=$f[3]; $sum_perc_id=$f[3]; } } elseif ($f[0]==$c && $f[1]<=($e+$tol)) { // join of current fragment with prev $subfrags++; // incrementing counter of fragments joined $e=$f[2]; if (count($f)>=4) { if ($f[3]<$min_perc_id) $min_perc_id=$f[3]; $sum_perc_id+=$f[3]; } } else { // join not possible $match=fragmatchqtl($c,$s,$e,$qtlsp); // search for overlapping QTLs in target species array_push($reshis,array("chr"=>$c, "s"=>$s, "e"=>$e, "mc"=>$match[0]['chr'], "ms"=>$match[0]['s'], "me"=>$match[0]['e'], "mn"=>$match[0]['n'], "gen"=>$match[0]['mrk'])); $subfrags=1; // resetting counter of fragments that are joined $c=$f[0]; $s=$f[1]; $e=$f[2]; if (count($f)>=4) { $min_perc_id=$f[3]; $sum_perc_id=$f[3]; } } } // foreach $match=fragmatchqtl($c,$s,$e,$qtlsp); array_push($reshis,array("chr"=>$c, "s"=>$s, "e"=>$e, "mc"=>$match[0]['chr'], "ms"=>$match[0]['s'], "me"=>$match[0]['e'], "mn"=>$match[0]['n'], "gen"=>$match[0]['mrk'])); return $reshis; } #######################-------- Rip QTLs ---------####################### function ripqtl ($qtlsp) { $intermediate=array(); $res_qtlsp=array(); $single=array(); $intermediate=split("\n",$qtlsp); foreach ($intermediate as $q){ $single=split("\t",$q); if ($single[0]!=""){ array_push($res_qtlsp,$single); } } return $res_qtlsp; } #######################-------- Associative Array of QTLs ---------####################### function assqtl($siz,$name) { if (empty($siz) || empty($name)){ echo "Array zum assoziieren ist leer"; mysql_close($connect); mysql_close($connectQTL); exit; } $res=array(); $tmp=array(); $c1=count($siz); $c2=count($name); if ($c1!=$c2) { echo "Array zum assoziieren ist von falscher Laenge"; mysql_close($connect); mysql_close($connectQTL); exit; } for ($i=0;$i<$c1;$i++){ $tmp=array($name[$i]=>$siz[$i]); $res=array_merge($res,$tmp); } return($res); } #######################-------- Randomize QTLs ---------####################### function randomqtls($chromosomes,$qtls) { if(!is_array($chromosomes)) { echo "

Chromosomes must be defined as array ID => length, not as "; print_r($chromosomes); echo "

"; mysql_close($connect); mysql_close($connectQTL); exit; } $totallength=0; $res=array(); foreach($chromosomes as $n=>$l) { if ("0"==$n){ echo "oh, Chromosome==0"; mysql_close($connect); mysql_close($connectQTL); exit; } $res[$n]=intval($l/1000); } $chromosomes=$res; $res=array(); foreach($qtls as $n=>$l) { if ("0"==$n){ print_r($qtls); echo "
Chromosome==0"; mysql_close($connect); mysql_close($connectQTL); exit; } $res[$n]=intval($l/1000); } $qtls=$res; $newpos=array(); foreach($chromosomes as $n=>$c) { $totallength += $c; } foreach($qtls as $n=>$l) { $newpos[$n]=array(); $newpos[$n]["sum"]=mt_rand(1,$totallength-1);#*1000; $partsum=0; foreach($chromosomes as $c=>$cl) { $partsum+=$cl; if ($partsum>$newpos[$n]["sum"]) { $newpos[$n]["n"]=$n; $newpos[$n]["l"]=$l; $newpos[$n]["c"]=$c; if (0==$c){ echo "oh, oh Chromosome=0"; mysql_close($connect); mysql_close($connectQTL); exit; } $newpos[$n]["p"]=$newpos[$n]["sum"]+$cl-$partsum; if ($newpos[$n]["p"]+$l>$cl) { $newpos[$n."'"]=array(); $newpos[$n."'"]["c"]=$c; $newpos[$n."'"]["n"]=$n; $newpos[$n."'"]["l"]=$l-($cl-$newpos[$n]["p"]); $newpos[$n."'"]["p"]=1; } break; } } $newpos[$n]["sum"]=mt_rand(1,$totallength-1);#*1000; $i++; } $qtlstring=array(); foreach ($newpos as $n=>$a) { array_push($qtlstring,$a["c"],($a["p"]*1000),(($a["p"]+$a["l"])*1000),($a["n"])); } return $qtlstring; }//function randomqtls #######################-------- Retrieve Merged! QTLs ---------####################### function retrieveqtls($organism="Mus_musculus",$db="qtl"){ global $metatrait; global $centroid; $checklist=array(); global $connectQTL; echo "metatrait:".$metatrait."
"; if ($centroid=="on") $queryQTLs="SELECT chr,start_centroid,stop_centroid,name FROM "; else $queryQTLs="SELECT chr,start_bps,stop_bps,name FROM "; switch(strtolower($metatrait)) { case 'cia': $queryQTLs .= "cia_qtl"; break; case 'CIA': $queryQTLs .= "cia_qtl"; break; case 'eae': $queryQTLs .= "eae_qtl"; break; case 'EAE': $queryQTLs .= "eae_qtl"; break; case 'games': $queryQTLs .= "gam_qtl"; break; case 'GAMES': $queryQTLs .= "gam_qtl"; break; case 'ms': $queryQTLs .= "ms_qtl"; break; default: echo "

Please specify metatrait.

"; exit; } $queryQTLs .= " WHERE species='$organism' "; # definiere organism if (!mysql_select_db($db,$connectQTL)) { echo "Could not select database on server."; exit; } $result=mysql_query($queryQTLs,$connectQTL); if (!$result) { echo "Could not execute query for QTLs'$queryQTLs'"; exit; } $txt4screen=array(); for ($i=0; $n=mysql_fetch_row($result); $i++) { if ($n[1]>$n[2]) { $tmp=$n[1]; $n[1]=$n[2]; $n[2]=$tmp; } $txt4screen[]=$n; } mysql_free_result ($result); $txt=array(); $i=0; $rows=4; #echo "count: ".count($txt4screen); #print_r($txt4screen); for ($j=0;$j EMPTY "; } else { $txt=$mergedqtls; $mergedqtls=array(); } $change=0; $first=1; foreach ($txt as $t) { if ($first==1) { array_push($mergedqtls,$t); $first=0; } else{ $flag=0; if ($t[1]==0 && $t[2]==0) continue; $limitcount=count($mergedqtls); for ($j=0;$j<=$limitcount;$j++) { if ($t[0]==$mergedqtls[$j][0] && $t[1]<=$mergedqtls[$j][1] && $t[2]>=$mergedqtls[$j][1] ){ # expand start $mergedqtls[$j][1]=$t[1]; $flag=1; $change=1; } if ($t[0]==$mergedqtls[$j][0] && $t[2]>=$mergedqtls[$j][2] && $t[1]<=$mergedqtls[$j][2] ) { $mergedqtls[$j][2]=$t[2]; $flag=1; $change=1; } # expand end if ($flag==1) continue; elseif ($j==$limitcount) { #echo "
no expand"; array_push($mergedqtls,$t); } } } } }# end of while return $mergedqtls; } #######################-------- Read QTLs ---------####################### function readqtls($string) { $arr1=array(); $arr2=array(); $rows=preg_split("/[\n\r]+/",$string); $i=0; foreach ($rows as $r) { $i++; $arr1=preg_split("/[ \t]+/",$r); $arr2[$arr1[3].$i]=array($arr1[0],$arr1[1],$arr1[2],($arr1[3]."-".$i)); if ("0"==$arr1[3]) { echo "wir haben die Fehlerquelle in readqtls"; print($r); echo "arr1[0]: ".$arr1[0]."arr1[1]: ".$arr1[1]."arr1[2]: ".$arr1[2]."arr1[3]: ".$arr1[3]; exit; } } return $arr2; } ########################################## MAIN ################################################## echo "

QTLs and SLs submitted

"; $doit="no"; if (is_string($qtlsp1)) $doit="yes"; elseif ($metatrait!="-no") $doit="yes"; if ($doit=="yes") { # MYSQL QUERY ON QTL DBASE if (empty($qtlsp1)) $qtlsp1=getqtls("qtl","",$sp1); else $qtlsp1=ripqtl($qtlsp1); if ($sp2!="----none----") { if (empty($qtlsp2)) $qtlsp2=getqtls("qtl","",$sp2); else $qtlsp2=ripqtl($qtlsp2); } if (empty($qtlsp3)) $qtlsp3=getqtls("qtl","",$sp3); else $qtlsp3=ripqtl($qtlsp3); if ($sp2!="----none----") { $controlc=0; $controls=0; foreach ($qtlsp2 as $qsp) { if ($controlc==$qsp[0] && $controls==$qsp[1]); else { if (empty($qsp[4])) $qsp[4]=chop($qsp[3]); array_push($sp2LinkToExpressionview, array("chr"=>($qsp[0]), "name"=>(chop($qsp[4]).":".$sp2), "s"=>($qsp[1]), "e"=>($qsp[2]), "t"=>"QTL/SL region" ) ); } $controlc=$qsp[0]; $controls=$qsp[1]; } } $controlc=0; $controls=0; foreach ($qtlsp3 as $qsp) { if ($controlc==$qsp[0] && $controls==$qsp[1]); else { if (empty($qsp[4])) $qsp[4]=chop($qsp[3]); array_push($sp3LinkToExpressionview, array("chr"=>($qsp[0]), "name"=>(chop($qsp[4]).":".$sp3), "s"=>($qsp[1]), "e"=>($qsp[2]), "t"=>"QTL/SL region" ) ); } $controlc=$qsp[0]; $controls=$qsp[1]; } $consensus_locations=array(); $count_consensus=0; $count_consensus_c2=0; $bps_size_c2=0; $frag_number_c2=0; $frag_number_c3=0; $joined_frag_number_c2=0; $joined_frag_number_c3=0; } // if meta=none $control_size="no"; if (is_array($qtlsp1)){ if (count($qtlsp1)>0 && count($qtlsp3)>0) { if (count($qtlsp1[0])>3 && count($qtlsp3[0])>3) $control_size="ok"; } } ###### DISPLAY OF THE CURRENT QTLs: ####### ################ RETRIEVES THE CURRENT QTL POSITIONS (Random or not) ############## echo "

\n"; if ($control_size!="ok" ){ echo "Please paste your QTLs and SLs in the corresponding textareas and click on the refresh button
"; echo "

"; echo "Back to qtl.pzr.uni-rostock.de"; echo ", for feedback or assistance please contact Pablo Serrano-Fernández or Steffen Möller\n"; exit; } # MYSQL QUERY ON COMPARA DBASE , FRAGMENTS JOINING , DISPLAY echo ""; if ($sp2!="----none----") { echo ""; } echo ""; echo ""; echo ""; if ($sp2!="----none----") { echo ""; echo ""; } echo ""; if ($sp2=="----none----") { foreach ($qtlsp1 as $q) { array_push($joined,array("mc"=>($q[0]),"ms"=>($q[1]), "me"=>($q[2]), "mn"=>($q[3]))); } } foreach ($qtlsp1 as $q) { if ($sp2!="----none----") { $frags=getfrags($q[0],$q[1],$q[2],$sp1,$sp2,$afn); $joined=joinfrags($frags,$qtlsp2); $frag_number_c2+=count($frags); $joined_frag_number_c2+=count($joined); } foreach ($joined as $joinedl) { $controlc=0; $controls=0; if (!empty($joinedl['ms'])) { $count_consensus_c2++; echo ""; if ($sp2!="----none----") $size_4_table1=intval(($q[2]-$q[1])/1000); else $size_4_table1=intval(($joinedl['me']-$joinedl['ms'])/1000); if ($size_4_table1<1) $size_4_table1="0.5"; echo ""; if ($sp2!="----none----") { echo ""; # QTL match echo ""; $bps_size_c2+=($joinedl['me']-$joinedl['ms']); } # TARGET SPECIES match if ($sp2!="----none----") $hmfrags=getfrags($joinedl['mc'],$joinedl['ms'],$joinedl['me'],$sp2,$sp3,$afn2); else $hmfrags=getfrags($joinedl['mc'],$joinedl['ms'],$joinedl['me'],$sp1,$sp3,$afn2); $frag_number_c3+=count($hmfrags); if (0

$sp1 QTLs

"; echo "Homology in $sp2

Homology in $sp3

Chr.

Kbp Start

Kbp Size

Name

Chr.

Kbp Start

Kbp Size

Consensus

"; echo ""; echo "

Chr.	Kbp Start	Kbp Size	Consensus

"; if ($sp2!="----none----") echo $q[0]; else echo $joinedl['mc']; echo "

"; if ($sp2!="----none----") echo intval($q[1]/1000); else echo intval($joinedl['ms']/1000); echo "

".$size_4_table1."

"; if ($sp2!="----none----") echo $q[3]; else echo $joinedl['mn']; echo "

".$joinedl['chr']."

".intval($joinedl['s']/1000); $size_4_table2=intval(($joinedl['e']-$joinedl['s'])/1000); if ($size_4_table2<1) $size_4_table2="0.5"; echo "

".$size_4_table2."

"; echo ''; echo intval($joinedl['ms']/1000); echo "-".intval($joinedl['me']/1000).""; echo " (".$joinedl['mn'].")"; echo "

"; foreach ($joinedhm as $joinedhmi) { if (0==$joinedhmi['s']) continue; echo ""; echo ""; echo ""; # Incase we have consensus susceptibility regions for the target species # if (!empty($joinedhmi['mc'])) { echo ""; if ($controlc==$joinedl['mc'] && $controls==$joinedl['ms']) continue; if ($sp2!="----none----") { array_push($sp2LinkToExpressionview, array("chr"=>($joinedl['mc']), "name"=>(chop($joinedl['mn']).":".$sp2), "s"=>($joinedl['ms']), "e"=>($joinedl['me']), "t"=>"Consensus QTL with source species" ) ); } $controlc=$joinedl['mc']; $controls=$joinedl['ms']; } echo ""; } echo "

"; echo ''; echo $joinedhmi['chr']."

"; echo ''; echo (intval(($joinedhmi['s'])/1000))."

"; echo ''; $size_4_table3=intval(($joinedhmi['e']-$joinedhmi['s'])/1000); if ($size_4_table3<1) $size_4_table3="0.5"; echo $size_4_table3."

"; if (0==$joinedhmi['ms']) continue; echo ""; # for further analyses $count_consensus++; array_push($consensus_locations, array("n"=>($count_consensus), "chr"=>($joinedhmi['mc']), "s"=>($joinedhmi['ms']), "e"=>($joinedhmi['me']))); if ($controlc==$joinedl['mc'] && $controls==$joinedl['ms']); else { if (empty($joinedhmi['gen'])) $joinedhmi['gen']=chop($joinedhmi['mn']); if ($sp2!="----none----"){ array_push($sp2LinkToExpressionview, array("chr"=>($joinedl['mc']), "name"=>(chop($joinedl['mn']).":".$sp2), "s"=>($joinedl['ms']), "e"=>($joinedl['me']), "t"=>"Consensus with source species" ) ); $txt_4_Exview="Consensus with source and intermediate species"; } else $txt_4_Exview="Consensus with source species"; array_push($sp3LinkToExpressionview, array("chr"=>($joinedhmi['mc']), "name"=>(chop($joinedhmi['gen']).":".$sp3), "s"=>($joinedhmi['ms']), "e"=>($joinedhmi['me']), "t"=>($txt_4_Exview) ) ); } $controlc=$joinedl['mc']; $controls=$joinedl['ms']; echo "

"; echo ''; */ echo '"; echo "

'; /* ---------------------------------------------------------------- Momentarily knocked out $line="http://ensembl.pzr.uni-rostock.de/Homo_sapiens/martview?"; echo '

'; echo ''.intval($joinedhmi['ms']/1000); echo "-".intval($joinedhmi['me']/1000); if (!empty($joinedhmi['gen'])) echo " (".chop($joinedhmi['gen']).")"; else echo " (".chop($joinedhmi['mn']).")"; echo "

"; } else { echo "

"; /* -------------------------------------------------------------------- Momentarily knocked out echo ''; */ echo "

'; $line="http://ensembl.pzr.uni-rostock.de/Multi/martview/tv2GFJbsqz.mart"; echo '

no match

";#
"; //} if ($sp2=="----none----") $org_names=array("sp3"); else $org_names=array("sp2","sp3"); foreach ($org_names as $org) { echo "

Consensi in ".$$org."

\n"; echo "

"; echo "

\n"; echo "\n"; echo "

"; } ############################################################################################################################################ ######################################## Genes in the consensus regions of the target species ############################################## ############################################################################################################################################ echo "

Consensus genes

"; echo "

\n"; echo '

if (!mysql_select_db("ensembl_mart_16_1",$connect)) {
	echo "Could not select database on server.";
	exit;
 }

$total_bps_c3=0;
$smart_list=array();
$count_genes=0;
$check_list=array();

$arr_sp3=array();
$arr_sp3=split("_",strtolower($sp3));
$main_dbase=substr($arr_sp3[0],0,1).$arr_sp3[1]."_ensemblgene_main";

foreach ($consensus_locations as $i){
  if ($sp3=="Homo_sapiens" && ($i['chr']=="X" || $i['chr']=="x")) $i['chr']=23;
  if ($sp3=="Homo_sapiens" && ($i['chr']=="Y" || $i['chr']=="y")) $i['chr']=24;
  if ($sp3=="Mus_musculus" && ($i['chr']=="X" || $i['chr']=="x")) $i['chr']=20;
 
  $total_bps_c3+=($i['e']-$i['s']);

//        -------------------------- Warning ---> query only in hsapiens_ensemblgene_main!! ---------------------------

$query="SELECT gene_stable_id_v, display_id, gene_chrom_start, gene_chrom_end 
	FROM ".$main_dbase." 
	WHERE chromosome_id=".$i['chr']." 
	AND ((gene_chrom_start<=".$i['s']." AND gene_chrom_end>=".$i['s'].") OR (gene_chrom_start<=".$i['e']." AND gene_chrom_end>=".$i['e'].")
	  OR (gene_chrom_start>=".$i['s']." AND gene_chrom_end<=".$i['e'].") 
	    )";
   $result=mysql_query($query,$connect);
    if (!$result) {
    		 echo "<p><font color=#cc0000>Could not execute query '$query'</font></p>";
       		 exit;
    }
   for ($f=0; $n=mysql_fetch_row($result); $f++) {                        
	$compare_str=strval($n[0]);
	if (in_array($compare_str,$check_list));
	else {
	 array_push($smart_list,
	 array("ens"=>($n[0]),
	       "ext"=>($n[1]),
               "s"=>($n[2]),
	       "e"=>($n[3]),
	       "chr"=>($i['chr'])
	       ));
	 $count_genes++;      
	 array_push($check_list,$n[0]);
	 echo $n[0]." ".$n[1];
	 echo "\n";
	}      
    }
    mysql_free_result ($result);

}
echo "

"; echo "\n"; echo "\n"; echo "

"; echo "

Summary

\n
"; echo "

"; echo "Kbp in consensus (all species): ".intval($total_bps_c3/1000); echo "

"; echo "Genes in consensus (all species): ".$count_genes; echo "

"; echo "Fragments (not joined) in consensus (sp1+sp2+ sp3_only_synt): ".$frag_number_c3; echo "	"; echo "Fragments (joined) in consensus (sp1+sp2+ sp3_only_synt): ".$joined_frag_number_c3; echo "
"; echo "Fragments (not joined) in consensus (all species): not queried"; echo "	"; echo "Fragments (joined) in consensus (all species): ".$count_consensus; echo "
"; echo "Kbp in consensus (sp1+sp2): ".intval($bps_size_c2/1000); echo "	"; echo "Genes in consensus (sp1+sp2): not queried"; echo "
"; echo "Fragments (not joined) (sp1+sp2): ".$frag_number_c2; echo "	"; echo "Fragments (joined) (sp1+sp2): ".$joined_frag_number_c2; echo "
"; echo "Fragments (not joined) in consensus (sp1+sp2): not queried "; echo "	"; echo "Fragments (joined) in consensus (sp1+sp2): ".$count_consensus_c2; echo "

"; echo "
"; echo "

"; echo "

Back to qtl.pzr.uni-rostock.de, for feedback or assistance please contact "; echo "Pablo Serrano-Fernández or Steffen Möller\n"; mysql_close($connect); ?>

QTLs and SLs submitted

Stepwise Intergenomic Consensus

$sp1 QTLs

"; echo "Homology in $sp2

Homology in $sp3

Consensi in ".$$org."

Consensus genes

Summary