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Sequences in red contain non-standard nucleotides.
Click on the virus name to see an image.\n"; $q = "select distinct viper.entry_key, pdb_id, entry_id, name from viper,ENTITY_POLY where viper.entry_key = ENTITY_POLY.entry_key and type like '%nucleotide%' and family = '$family'"; $results = @mysql_query($q); $entries = array(); while ($row = mysql_fetch_assoc($results)) { array_push($entries,$row); } $data = array(); foreach ($entries as $entry) { $sequences = array(); $lengths = array(); $types = array(); $entry_key = $entry['entry_key']; $data[$entry_key] = array(); $next = "select type, pdbx_seq_one_letter_code, number_of_monomers, nstd_monomer, entity_key from ENTITY_POLY where entry_key = $entry_key and type like '%nucleotide%'"; $results2 = @mysql_query($next); while ($nrow = mysql_fetch_array($results2)) { // Get the chain ID for the entity $entity_key = $nrow['entity_key']; $lq = "select label_asym_id from ATOM_SITE where entry_key = $entry_key and label_entity_key = $entity_key limit 1"; // print "$lq
"; $lek = @mysql_query($lq); $lrow = mysql_fetch_row($lek); $chainid = $lrow[0]; // print "Done query.
Freeing result
"; mysql_free_result($lek); // print "Done freeing result.
"; // if ($nrow['nstd_monomer'] == "no") { array_push($sequences,$chainid."(".$nrow['pdbx_seq_one_letter_code'].")"); } else { array_push($sequences,$chainid."("."".$nrow['pdbx_seq_one_letter_code']."".")"); } $nucname = $nrow['type']; //Not in database, must find the length //$length = $row['number_of_monomers']; $aSeq = preg_split('//', $nrow['pdbx_seq_one_letter_code'], -1, PREG_SPLIT_NO_EMPTY); $length = 0; $inParen = false; foreach($aSeq AS $c){ if($c == '('){ $length++; $inParen = true; } if($inParen == false){ $length++; } if($c == ')'){ $inParen = false; } } array_push($lengths,$chainid."(".$length.")"); switch($nucname) { case 'polydeoxyribonucleotide': $dorn = 'DNA'; break; case 'polyribonucleotide': $dorn = 'RNA'; break; default: $dorn = '???'; break; } array_push($types,$dorn); } // Only one instance of each type should be listed. $types = array_unique($types); $data[$entry_key]['sequences'] = join(", ",$sequences); $data[$entry_key]['types'] = join(", ",$types); $data[$entry_key]['lengths'] = join(", ",$lengths); } foreach ($entries as $entry) { $entry_key = $entry['entry_key']; $name = $entry['name']; print ""; print ""; print ""; print ""; print ""; print ""; print ""; } $count++; } print "
Virus Name

RNA/DNA

Sequence

# Nucleotides

PDB ID

$count. $family
".$entry['name']."".$data[$entry_key]['types']."".$data[$entry_key]['sequences']."".$data[$entry_key]['lengths']."".$entry['entry_id']."
"; // $results = @mysql_query("select distinct pdb_id, entry_id, name, type, pdbx_seq_one_letter_code, number_of_monomers, nstd_monomer from viper,ENTITY_POLY where viper.entry_key = ENTITY_POLY.entry_key and type like '%nucleotide%' order by family"); $results = @mysql_query("select distinct entry_id, name from viper,ENTITY_POLY where viper.entry_key = ENTITY_POLY.entry_key and type like '%nucleotide%' order by family"); print "

Stereo pictures: (click images to enlarge)


"; while ($row = mysql_fetch_array($results)) { $name = $row['name']; $entry_id = $row['entry_id']; $stereo = "rna_" . $entry_id . "_stereo.gif"; $mono = "rna_" . $entry_id . ".gif"; print ""; print ""; } ?>
$name
$name

$name stereo
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by Padmaja Natarajan
Last Modified : Tues Nov 8 11:58:20 PDT 2005