"; $db_pai = mysql_query($query, $db_conn); list ($species, $strain, $name, $func, $pai_remark, $insSite) = mysql_fetch_row($db_pai); if (!$func) $func = "Unassigned"; $func = preg_replace("/\"/","",$func); $func = preg_replace("/alpha-/","α-",$func); $func = preg_replace("/beta-/","β-",$func); $func = preg_replace("/gamma-/","γ-",$func); $func = preg_replace("/delta-/","δ-",$func); $func = preg_replace("/omega-/","ω-",$func); $func = preg_replace("/lambda-/","λ-",$func); $func = preg_replace("/phi-/","φ-",$func); $func = preg_replace("/pi-/","π-",$func); $func = preg_replace("/sigma-/","σ-",$func); $func = preg_replace("/_alpha/","α",$func); $func = preg_replace("/_beta/","β",$func); $func = preg_replace("/_gamma/","γ",$func); $func = preg_replace("/_delta/","δ",$func); $func = preg_replace("/_omega/","ω",$func); $func = preg_replace("/_lambda/","λ",$func); $func = preg_replace("/_phi/","φ",$func); $func = preg_replace("/_pi/","π",$func); $func = preg_replace("/_sigma/","σ",$func); $func = preg_replace("/alpha_/","α",$func); $func = preg_replace("/beta_/","β",$func); $func = preg_replace("/gamma_/","γ",$func); $func = preg_replace("/delta_/","δ",$func); $func = preg_replace("/omega_/","ω",$func); $func = preg_replace("/lambda_/","λ",$func); $func = preg_replace("/phi_/","φ",$func); $func = preg_replace("/pi_/","π",$func); $func = preg_replace("/sigma_/","σ",$func); $name = preg_replace("/alpha-/","α-",$name); $name = preg_replace("/beta-/","β-",$name); $name = preg_replace("/gamma-/","γ-",$name); $name = preg_replace("/delta-/","δ-",$name); $name = preg_replace("/omega-/","ω-",$name); $name = preg_replace("/lambda-/","λ-",$name); $name = preg_replace("/phi-/","φ-",$name); $name = preg_replace("/pi-/","π-",$name); $name = preg_replace("/sigma-/","σ-",$name); $name = preg_replace("/_alpha/","α",$name); $name = preg_replace("/_beta/","β",$name); $name = preg_replace("/_gamma/","γ",$name); $name = preg_replace("/_delta/","δ",$name); $name = preg_replace("/_omega/","ω",$name); $name = preg_replace("/_lambda/","λ",$name); $name = preg_replace("/_phi/","φ",$name); $name = preg_replace("/_pi/","π",$name); $name = preg_replace("/_sigma/","σ",$name); $name = preg_replace("/alpha_/","α",$name); $name = preg_replace("/beta_/","β",$name); $name = preg_replace("/gamma_/","γ",$name); $name = preg_replace("/delta_/","δ",$name); $name = preg_replace("/omega_/","ω",$name); $name = preg_replace("/lambda_/","λ",$name); $name = preg_replace("/phi_/","φ",$name); $name = preg_replace("/pi_/","π",$name); $name = preg_replace("/sigma_/","σ",$name); $query = "SELECT pai_accn, gi, size, no_orf, flag_full, definition FROM pai_record WHERE id_paii='$pn' "; $db_pir = mysql_query($query, $db_conn); $npir = mysql_num_rows($db_pir); # homologous genome #$querym = "SELECT distinct si.species, si.strain, gp.genome_accn, gp.gstart # FROM strain_info as si, genome as g, genome_plr as gp, pai_strip as ps # WHERE ps.paii_id='$pn' # AND ps.genome_plr_id=gp.genome_plr_id AND ps.genome_accn=gp.genome_accn AND gp.genome_accn=g.genome_accn # AND g.strain_id=si.strain_id AND gp.vir='V' # ORDER BY si.species ASC, si.strain ASC, gp.genome_accn ASC, gp.gstart ASC "; $querym = " SELECT distinct si.species, si.strain, gp.genome_accn, gp.id_plr, gp.vir, gp.position_begin_genome FROM strain_class as si, genome_plr as gp, pai_strip as ps WHERE ps.id_paii='$pn' AND si.chromosom_accn=ps.genome_accn AND gp.id_plr=ps.id_plr AND ps.genome_accn=gp.genome_accn AND gp.vir='V' ORDER BY si.species ASC, si.strain ASC, gp.genome_accn ASC, gp.position_begin_genome ASC; "; #SELECT distinct si.species, si.strain, gp.genome_accn, gp.id_plr, gp.vir, gp.position_begin_genome # FROM strain_class as si, genome_plr as gp, pai_strip as ps # WHERE ps.id_paii='$pn' # AND gp.id_plr=ps.id_plr AND ps.genome_accn=gp.genome_accn AND gp.genome_accn=g.genome_accn # AND ps.id_paii='$pn' AND gp.vir='V' # ORDER BY si.species ASC, si.strain ASC, gp.genome_accn ASC, gp.gstart ASC #echo "$querym
\n"; $db_pig= mysql_query($querym, $db_conn); $npig = mysql_num_rows($db_pig); # reporting if($insSite=="NP") $insSite="Not published"; echo "

"; if($func=="Not published") echo"Unconfirmed "; if($m=="r"||$m=="g"||$m=="p") echo "Pathogenicity Island: $name

"; else echo "Pathogenicity Island: $name "; echo"

• General information

Name : $name
\n Host strain : $species $strain
\n Function : $func
\n Insertion site : $insSite
\n

"; echo"

• GenBank accessions: $npir records

\n"; for ($pir=1;$pir<=$npir;$pir++) { list ($pir_accn, $pir_gi, $pir_length, $nprotein, $flag_full, $pir_remark) = mysql_fetch_row($db_pir); # get the referenece information include ("db_global.php"); $query = "select * from reference ". "where accn='$pir_accn' "; $db_pref = mysql_query($query, $db_conn); $npref = mysql_num_rows($db_pref); mysql_close($db_conn); if(preg_match("/_P[0-9]/", $pir_accn)) echo"

$pir) $pir_accn ($pir_length bp)

"; else echo"

$pir) $pir_accn ($pir_length bp)

"; echo "
    Definition : $pir_remark

    Publication :
    "; for($pref=1;$pref<=$npref;$pref++) { list ($pref_no, $paccn, $author, $title, $journal, $medline, $pubmed) = mysql_fetch_row($db_pref); echo "- $author, \"$title\", "; if ($pubmed&&$medline) echo "$journal"; else echo "$journal"; echo ".

    \n"; } echo "

      

"; $nmap = (int)($pir_length/$vrange)+1; $range_start = 1; $range_end = 0; for($i=0;$i<$nmap-1;$i++){ $range_end += $vrange; $map_name = "paimap$i"; draw_pai_imap($range_start, $range_end, $pir_accn, $map_name, $m); echo"
"; $range_start = $range_end; } if ($pir_length<$vrange) $range_end=((int)($pir_length/1000) +1) *1000; else $range_end += $vrange; #$bend = $pir_length; $map_name = "paimap$pir"."__$i"; draw_pai_imap($range_start, $range_end, $pir_accn, $map_name, $m); echo"

"; include ("db_global.php"); #$query = "SELECT pid, gi, po.name, name_alt, start, end, strand, length, product, func, note, po.remark, vir, po.orf_tcode, ot.name, pai_orf_id $query = "SELECT pid, gi, po.name, name_alt, begin, end, strand, size, product, function, note, po.remark, vir, po.type, ot.remark, id_pai_orf FROM pai_orf as po, orf_type_code as ot WHERE pai_accn='$pir_accn' AND po.type=ot.type "; #echo "$query
"; $db_gnp = mysql_query($query, $db_conn); $ngnp = mysql_num_rows($db_gnp); mysql_close($db_conn); echo "

\n"; } echo "

• PAI-like regions homologous to this PAI (genomes and locations)

\n
"; if ($npig) { $genome0=""; for ($pig=0;$pig<$npig;$pig++) { #list($gsp, $gst, $genome_accn, $gp_id, $gms, $vir, $bstart) = mysql_fetch_array($db_pig); list($gsp, $gst, $genome_accn, $gp_id, $vir, $bstart) = mysql_fetch_array($db_pig); $stst="$gsp $gst"; #if($pig) echo ",   "; $posit = sprintf("%.1f",$bstart/1000000.); #if($genome0==$genome_accn) echo ", $posit"; if($vir=="V") $cn_type="c"; else $cn_type="n"; if($genome0==$genome_accn) echo ", $posit"; else { if($genome0) echo " Mb
\n"; echo "$genome_accn ($stst): $posit"; } $genome0=$genome_accn; #$stst0=$stst; } echo " Mb
\n"; } else echo "None"; echo "
\n
"; /* #------------------------------------------------------ if($ngene) { echo"Members Genes"; for($i=0;$i<$ngene;$i++) { list ($gene_accn, $gi, $name, $name_alt, $product) = mysql_fetch_row($db_gene); $product = preg_replace ("/\[.+\]/", "", $product); if($name=="-") $name=$name_alt; echo "$name$gene_accn$product\n"; } } if($nstr) { echo "Members Other Structures"; for($i=0;$i<$nstr;$i++) { list ($str_name, $name, $product) = mysql_fetch_row($db_str); #$product = preg_replace ("/\[.+\]/", "", $product); #if($name=="-") $name=$name_alt; echo "$name$str_name$product\n"; } } echo " \n \n "; */ #--------------------------------------------------------- include "bottom.php"; ?>