Genome Information\n"; if (!$gma) $gma="NC_002745"; $genome_accn = $gma; $itemNo = 1; # open db connection include ("db_global.php"); # Genome information #- $query = "SELECT genome_accn, genome_scode, gps.species, gps.strain, genome_gi, size_genome, no_protein, pathogenicity, remark, gc_content, gi $query = "SELECT genome_accn, genome_scode, gps.species, gps.strain, size_genome, no_protein, pathogenicity, disease, gc_content FROM genome_pai_stat as gps WHERE genome_accn='$gma'"; #echo "$query
\n"; $db_res = mysql_query($query, $db_conn); list ($genome_accn, $genome_type, $species, $strain, $genome_length, $nprotein, $pathogen, $remark, $gcc) =mysql_fetch_row($db_res); $query = "SELECT * FROM genome_shape_code WHERE genome_scode='$genome_type'"; $db_res = mysql_query($query, $db_conn); list ($genome_type, $type_remark) = mysql_fetch_row($db_res); echo "

• General information



• PAIs (PAI reported to be located in this genome)

"; $no = 0; if($nres1) { echo " \n"; while(list($pNameP, $pstart, $pend, $plength, $piInsSite, $piFunc, $piPaiiId)=mysql_fetch_array($res1)) { $no++; if(!$piInsSite) $piInsSite="-"; if(!$piFunc) $piFunc="-"; $piFunc=preg_replace("/\"/","",$piFunc); #echo " echo "\n"; } echo"
No Name Start End Size(bp)Insertion SiteFunction
$no $pNameP
$no $pNameP $pstart$pend$plength$piInsSite$piFunc
"; } else echo "
   Not Found.\n"; # -------------------------- # print cPAI table on Genome /* # FROM genome as g, genome_plr as gp # WHERE g.genome_accn=gp.genome_accn AND gp.genome_accn='$genome_accn' AND gp.gms='G' AND gp.vir='V' SELECT species, strain, pathogenicity, gps.genome_accn, count(distinct gp.id_plr) FROM genome_pai_stat as gps, genome_plr as gp WHERE gps.genome_accn=gp.genome_accn AND gp.vir='V' AND gp.id_gi>0 GROUP BY species ASC, strain ASC, gp.genome_accn ASC */ $query2 = "SELECT distinct id_plr, vir, position_begin_genome, position_end_genome, size, no_gorf, gp.gc_content FROM genome_plr as gp, genome_pai_stat as gps WHERE gps.genome_accn='$genome_accn' AND gps.genome_accn=gp.genome_accn AND (gp.vir='V' OR gp.vir like '%V') AND gp.id_gi>0 ORDER BY position_begin_genome ASC "; $res2 = mysql_query($query2, $db_conn); $nres2 = mysql_num_rows($res2); #echo "
$query2
\n"; $itemNo++; echo "

• cPAIs (PAI-like region overlapping genomic islands (candidate PAI))

  * Percentage of foreign genes which are biased in both G+C content and codon usage
"; $no=0; if($nres2) { echo " "; # while(list($gpid, $vir, $start, $end, $size, $nOrf, $gcc)=mysql_fetch_array($res2)) { $no++; #if(!$pNameG) $pNameG="-"; if(!$gpid) $gpid="-"; if(!$gms) $gms="-"; if(!$vir) $vir="-"; $query21= "SELECT count(*) FROM genome_orf WHERE $start<=begin AND end<=$end AND vir='V' AND genome_accn='$genome_accn' "; $res21 = mysql_query($query21, $db_conn); list($nVir)=mysql_fetch_array($res21); $query22= "SELECT distinct p.name, pi.id_paii, pi.species, pi.strain FROM genome_plr as gp, pai_strip as ps, pai_instance as pi, pai as p WHERE gp.genome_accn='$genome_accn' AND ps.genome_accn=gp.genome_accn AND gp.id_plr=ps.id_plr AND ps.id_paii=pi.id_paii AND pi.id_pai=p.id_pai AND $start<=gp.position_begin_genome AND gp.position_end_genome<=$end "; # FROM genome_plr as gp, pai_strip as ps, pai_instance as pi, pai as p, strain_info as si, genome as g # AND gp.genome_accn=g.genome_accn # echo "$query22
\n"; $res22 = mysql_query($query22, $db_conn); # #echo " echo "\n"; } echo"
No Start End Size(bp) No. of ORFs G+C
content
No. of homologs of PAI-virulence genes PAIs homologous to this region
Foreign genes*$start $end $size $nOrf $gcc %
$no
$no $start $end $size $nOrf $gcc % $nVir
"; $nres22 = mysql_num_rows($res22); if($nres22>0) { #javascript:open_PI('$piId')\">$pNameG ($sp $st)
"; #while(list($pNameG, $piId, $sp, $st)=mysql_fetch_array($res22)) echo "$pNameG ($sp $st)
"; while(list($pNameG, $piId, $sp, $st)=mysql_fetch_array($res22)) echo "$pNameG ($sp $st)
"; } else echo "None
"; echo " 
"; } else echo "
   Not Found.\n"; # -------------------------- # print nPAI table on Genome /* $query3 = "SELECT distinct gp.genome_plr_id, gp.gms, gp.vir, gp.gstart, gp.gend, gp.size, gp.no_gorf, gp.gc_content, gp.hgt_length_percent FROM genome as g, genome_plr as gp WHERE g.genome_accn=gp.genome_accn AND gp.genome_accn='$genome_accn' AND gp.vir='V' AND gp.gms!='G' ORDER BY gp.gstart ASC "; SELECT species, strain, pathogenicity, gps.genome_accn, count(distinct gp.id_plr) FROM genome_pai_stat as gps, genome_plr as gp WHERE gps.genome_accn=gp.genome_accn AND gp.vir='V' AND gp.id_gi=0 GROUP BY species ASC, strain ASC, gp.genome_accn ASC */ $query3 = "SELECT distinct id_plr, vir, position_begin_genome, position_end_genome, size, no_gorf, gp.gc_content FROM genome_pai_stat as gps, genome_plr as gp WHERE gps.genome_accn='$genome_accn' AND gps.genome_accn=gp.genome_accn AND (gp.vir='V' OR gp.vir like '%V') AND gp.id_gi=0 ORDER BY gp.position_begin_genome ASC "; #echo "$query3
\n"; $res3 = mysql_query($query3, $db_conn); $nres3 = mysql_num_rows($res3); $itemNo++; echo "

• nPAIs (PAI-like region not overlapping genomic islands (non-probable PAI))

  * Percentage of foreign genes which are biased in both G+C content and codon usage
"; $no=0; if($nres3) { echo " "; # #while(list($gpid, $gms, $vir, $start, $end, $size, $nOrf, $gcc, $hgt)=mysql_fetch_array($res3)) { while(list($gpid, $vir, $start, $end, $size, $nOrf, $gcc)=mysql_fetch_array($res3)) { $no++; #if(!$pNameG) $pNameG="-"; if(!$gpid) $gpid="-"; if(!$gms) $gms="-"; if(!$vir) $vir="-"; $query31= "SELECT count(*) FROM genome_orf WHERE $start<=begin AND end<=$end AND vir='V' AND genome_accn='$genome_accn' "; $res31 = mysql_query($query31, $db_conn); list($nVir)=mysql_fetch_array($res31); $query32= "SELECT distinct p.name, pi.id_paii, species, strain FROM pai as p, pai_instance as pi, pai_strip as ps, genome_plr as gp WHERE gp.genome_accn='$genome_accn' AND ps.genome_accn=gp.genome_accn AND gp.id_plr=ps.id_plr AND ps.id_paii=pi.id_paii AND pi.id_pai=p.id_pai AND $start<=gp.position_begin_genome AND gp.position_end_genome<=$end "; $res32 = mysql_query($query32, $db_conn); # #javascript:open_cnPai('$genome_accn','$gpid','n')\">$no echo "\n"; } echo"
No Start End Size(bp) No. of ORFs G+C
content
No. of homologs of PAI-virulence genes PAIs homologous to this region
Foreign genes*$start $end $size $nOrf $gcc %
$no $start $end $size $nOrf $gcc % $nVir
"; $nres32 = mysql_num_rows($res32); if($nres32>0) { #javascript:open_PI('$piId')\">$pNameG ($sp $st)
"; #while(list($pNameG, $piId, $sp, $st)=mysql_fetch_array($res22)) echo "$pNameG ($sp $st)
"; while(list($pNameG, $piId, $sp, $st)=mysql_fetch_array($res32)) echo "$pNameG ($sp $st)
"; } else echo "None
"; echo " 
"; } else echo "
   Not Found.\n

"; # ----------------------------- # print raw REI table on Genome $query4 = "SELECT pi.name, pr.position_begin_genome, pr.position_end_genome, pr.size, pi.insertion_site, pi.function, pi.id_paii FROM pai_instance as pi, pai_record as pr WHERE pr.pai_accn like '$genome_accn"."_%' AND pr.id_paii=pi.id_paii AND pi.data_source='genome' AND pi.classification='REI' ORDER BY pr.position_begin_genome ASC "; #echo "$query1
\n"; $res4 = mysql_query($query4, $db_conn); $nres4 = mysql_num_rows($res4); $itemNo ++; echo "

• REIs (REI reported to be located in this genome)

"; $no = 0; if($nres4) { echo " \n"; while(list($pNameP, $pstart, $pend, $plength, $piInsSite, $piFunc, $piPaiiId)=mysql_fetch_array($res4)) { $no++; if(!$piInsSite) $piInsSite="-"; if(!$piFunc) $piFunc="-"; $piFunc=preg_replace("/\"/","",$piFunc); #echo " echo "\n"; } echo"
No Name Start End Size(bp)Insertion SiteFunction
$no $pNameP
$no $pNameP $pstart$pend$plength$piInsSite$piFunc
"; } else echo "
   Not Found.\n"; # -------------------------- # print cREI table on Genome $query5 = "SELECT distinct id_plr, vir, position_begin_genome, position_end_genome, size, no_gorf, gp.gc_content FROM genome_plr as gp, genome_pai_stat as gps WHERE gps.genome_accn='$genome_accn' AND gps.genome_accn=gp.genome_accn AND (gp.vir='R' OR gp.vir like 'R%') AND gp.vir not like '%V' AND gp.id_gi>0 ORDER BY position_begin_genome ASC "; $res5 = mysql_query($query5, $db_conn); $nres5 = mysql_num_rows($res5); #echo "$query2
\n"; $itemNo++; echo "

• cREIs (REI-like region overlapping genomic islands (candidate REI))

  * Percentage of foreign genes which are biased in both G+C content and codon usage
"; $no=0; if($nres5) { echo " "; # while(list($gpid, $vir, $start, $end, $size, $nOrf, $gcc)=mysql_fetch_array($res5)) { $no++; #if(!$pNameG) $pNameG="-"; if(!$gpid) $gpid="-"; if(!$gms) $gms="-"; if(!$vir) $vir="-"; $query21= "SELECT count(*) FROM genome_orf WHERE $start<=begin AND end<=$end AND vir='R' AND vir not like '%V' AND genome_accn='$genome_accn' "; $res21 = mysql_query($query21, $db_conn); list($nVir)=mysql_fetch_array($res21); $query22= "SELECT distinct p.name, pi.id_paii, pi.species, pi.strain FROM genome_plr as gp, pai_strip as ps, pai_instance as pi, pai as p WHERE gp.genome_accn='$genome_accn' AND ps.genome_accn=gp.genome_accn AND gp.id_plr=ps.id_plr AND ps.id_paii=pi.id_paii AND pi.id_pai=p.id_pai AND $start<=gp.position_begin_genome AND gp.position_end_genome<=$end "; # echo "$query22
\n"; $res22 = mysql_query($query22, $db_conn); echo "\n"; } echo"
No Start End Size(bp) No. of ORFs G+C
content
No. of homologs of REI-resistance genes REIs homologous to this region
G+C
content
$no $start $end $size $nOrf $gcc % $nVir
"; $nres22 = mysql_num_rows($res22); if($nres22>0) { while(list($pNameG, $piId, $sp, $st)=mysql_fetch_array($res22)) echo "$pNameG ($sp $st)
"; } else echo "None
"; echo " 
"; } else echo "
   Not Found.\n"; # -------------------------- # print nREI table on Genome $query6 = "SELECT distinct id_plr, vir, position_begin_genome, position_end_genome, size, no_gorf, gp.gc_content FROM genome_pai_stat as gps, genome_plr as gp WHERE gps.genome_accn='$genome_accn' AND gps.genome_accn=gp.genome_accn AND (gp.vir='R' OR gp.vir like 'R%') AND gp.vir not like '%V' AND gp.id_gi=0 ORDER BY gp.position_begin_genome ASC "; #echo "$query3
\n"; $res6 = mysql_query($query6, $db_conn); $nres6 = mysql_num_rows($res6); $itemNo++; echo "

• nREIs (REI-like region not overlapping genomic islands (non-probable REI))

  * Percentage of foreign genes which are biased in both G+C content and codon usage
"; $no=0; if($nres6) { echo " "; # #while(list($gpid, $gms, $vir, $start, $end, $size, $nOrf, $gcc, $hgt)=mysql_fetch_array($res3)) { while(list($gpid, $vir, $start, $end, $size, $nOrf, $gcc)=mysql_fetch_array($res6)) { $no++; #if(!$pNameG) $pNameG="-"; if(!$gpid) $gpid="-"; if(!$gms) $gms="-"; if(!$vir) $vir="-"; $query31= "SELECT count(*) FROM genome_orf WHERE $start<=begin AND end<=$end AND vir='R' AND vir not like '%V' AND genome_accn='$genome_accn' "; $res31 = mysql_query($query31, $db_conn); list($nVir)=mysql_fetch_array($res31); $query32= "SELECT distinct p.name, pi.id_paii, species, strain FROM pai as p, pai_instance as pi, pai_strip as ps, genome_plr as gp WHERE gp.genome_accn='$genome_accn' AND ps.genome_accn=gp.genome_accn AND gp.id_plr=ps.id_plr AND ps.id_paii=pi.id_paii AND pi.id_pai=p.id_pai AND $start<=gp.position_begin_genome AND gp.position_end_genome<=$end "; /* $query32= "SELECT distinct p.name, pi.id_paii, species, strain FROM pai as p, pai_instance as pi, pai_strip as ps, genome_plr as gp WHERE gp.genome_accn='$genome_accn' AND gp.genome_plr_id=ps.genome_plr_id AND ps.paii_id=pi.paii_id AND pi.pai_id=p.pai_id AND si.strain_id=pi.strain_id AND ps.genome_accn=gp.genome_accn AND $start<=gp.gstart AND gp.gend<=$end ";*/ $res32 = mysql_query($query32, $db_conn); # #javascript:open_cnPai('$genome_accn','$gpid','n')\">$no echo "\n"; } echo"
No Start End Size(bp) No. of ORFs G+C
content
No. of homologs of REI-resistance genes REIs homologous to this region
G+C
content
$start $end $size $nOrf $gcc %
$no $start $end $size $nOrf $gcc % $nVir
"; $nres32 = mysql_num_rows($res32); if($nres32>0) { while(list($pNameG, $piId, $sp, $st)=mysql_fetch_array($res32)) echo "$pNameG ($sp $st)
"; } else echo "None
"; echo " 
"; } else echo "
   Not Found.\n

"; #echo "$query1
\n"; #echo "$query2
\n"; #echo "$query3
\n"; #echo "$query4
\n"; #echo "$query5
\n"; #echo "$query6
\n"; /* # make pai list for each species $query = "SELECT si.strain_id, species, strain, pi.paii_id, name, pi.remark, tend-tstart+1 FROM strain_info as si, pai as p, pai_instance as pi, genome_plr as gp WHERE genome_accn='$genome_accn' AND si.strain_id=pi.strain_id AND p.pai_id=pi.pai_id AND pi.paii_id=gp.paii_id ORDER BY name ASC "; echo "$query
\n"; $db_pths= mysql_query($query, $db_conn); $npth = mysql_num_rows($db_pths); if ($npth) { echo "

Pathogenicity Islands included in Genome $genome_accn


\n \n"; if($res1) while(list($sp, $st, $si, $pNameP, $piIdP)=mysql_fetch_array($res1)) { list($strain_id, $species, $strain, $paii_id, $name, $remark, $type, $length) = mysql_fetch_array($db_pths); if (!$remark) $remark = "-"; echo "\n"; } echo "
No PAI Name Remark Size Source Type Source Organism
$pth $name $remark $length $type $species $strain

\n"; } */ mysql_close($db_conn); ?>