Sequence ID $seqID\n";
}
else { // from protein.php
echo "
Feature ID $FeatureID
\n";
}
echo "\n";
$tax_id=$row[10];
$SEQ_id = $row[0];
$spname_enc = rawurlencode( $row[11]);
$result_t = FetchFromGOBASE( "select use_col from tax_lineage where tax_id = $tax_id", 1);
$row_t = pg_fetch_row( $result_t );
$col = $row_t[0];
$spname_anchor = "" .
"$row[11]";
$MoleculeType = $row[12];
$odd = 1;
$bgcolor = ($odd==1) ? "#ddddff" : "#D3DCE3";
echo "Species Name: | \n";
echo " $spname_anchor | \n";
echo "
\n";
$odd = ($odd==1)? 0 : 1;
$bgcolor = ($odd==1) ? "#ddddff" : "#D3DCE3";
echo "Molecular Type: | $MoleculeType | \n";
$odd = ($odd==1)? 0 : 1;
$bgcolor = ($odd==1) ? "#ddddff" : "#D3DCE3";
if($row[7] != '')
{
printf( "
Genbank Definition: | %s |
\n",
$row[7]);
$odd = ($odd==1)? 0 : 1;
$bgcolor = ($odd==1) ? "#ddddff" : "#D3DCE3";
}
if (trim($MoleculeType) =="aa") {
if ($row[13] !='') {
printf( "Product Name: | %s |
\n",
$row[13]);
$odd = ($odd==1)? 0 : 1;
$bgcolor = ($odd==1) ? "#ddddff" : "#D3DCE3";
}
}
$MapValue = "select substr(url,38) from map where seq_id = $SEQ_id";
$result1 = FetchFromGOBASE($MapValue, 1);
$row1 = pg_fetch_row($result1);
$Map_URL = $row1[0];
if($Map_URL != "") {
echo "Map: | $Map_URL |
\n";
$odd = ($odd==1)? 0 : 1;
$bgcolor = ($odd==1) ? "#ddddff" : "#D3DCE3";
}
$retrieve_criteria = "genome.php?Info=seq&SeqID=$SEQ_id";
echo "Plasmid: | $row[1] |
\n";
$odd = ($odd==1)? 0 : 1;
$bgcolor = ($odd==1) ? "#ddddff" : "#D3DCE3";
$reply = ($row[9]==1) ? "yes" : "no";
echo "Complete Genome: | $reply |
\n";
$odd = ($odd==1)? 0 : 1;
$bgcolor = ($odd==1) ? "#ddddff" : "#D3DCE3";
if ($FeatureID!="") { //for the link from protein.php only
echo "Sequence ID: | $seqID |
\n";
$odd = ($odd==1)? 0 : 1;
$bgcolor = ($odd==1) ? "#ddddff" : "#D3DCE3";
}
echo "Sequence Length: | $row[2] |
\n";
$odd = ($odd==1)? 0 : 1;
$bgcolor = ($odd==1) ? "#ddddff" : "#D3DCE3";
echo "Topology: | $row[3] |
\n";
$odd = ($odd==1)? 0 : 1;
$bgcolor = ($odd==1) ? "#ddddff" : "#D3DCE3";
if( $row[5] == "" )
{
$update = "n/a";
}
else
{
$pieces = explode( " ", $row[5] );
$update = $pieces[0] . " " . $pieces[1] . " " . $pieces[2];
}
if( $row[4] == "" )
{
$date = "n/a";
}
else
{
$pieces = explode( " ", $row[4] );
$date = $pieces[0] . " " . $pieces[1] . " " . $pieces[2];
}
echo "Submission Date: | $date |
\n";
$odd = ($odd==1)? 0 : 1;
$bgcolor = ($odd==1) ? "#ddddff" : "#D3DCE3";
if(!($update < $date)) {
echo "Update Date: | $update |
\n";
$odd = ($odd==1)? 0 : 1;
$bgcolor = ($odd==1) ? "#ddddff" : "#D3DCE3";
}
if(trim($MoleculeType) == 'aa'){
$db = 'protein';
$dopt = 'GenPept';
$ref_gi_sql ="select nagi from extprot where gi= $GI";#wol feb2010
$ref_gi_result = FetchFromGOBASE($ref_gi_sql, 1 );
$row_ref_gi = pg_fetch_row( $ref_gi_result );
$ref_gi=$row_ref_gi[0];
if(! $ref_gi) {$ref_gi = $GI;}#wol feb2010
}else{
$db = 'nucleotide';
$dopt = 'GenBank';
$ref_gi= $GI;#wol feb2010
}
echo "NCBI gi: | $GI |
\n";#wol feb2010
$odd = ($odd==1)? 0 : 1;
$bgcolor = ($odd==1) ? "#ddddff" : "#D3DCE3";
$acc = trim($row[6]);
echo "Genbank Accession: | $acc |
\n"; #wol feb2010
$odd = ($odd==1)? 0 : 1;
$bgcolor = ($odd==1) ? "#ddddff" : "#D3DCE3";
if($row[14] != ''){
echo "Author(s): | $row[14] |
\n";
}
$PID_record = "select pir_name from PIR where
PIR.seq_id = $SEQ_id";
$PID_result = FetchFromGOBASE($PID_record, 1 );
$row = pg_fetch_row( $PID_result );
$pir_acc = ($row[0]== "") ? "n/a" : $row[0];
$PID_link ="$pir_acc";
if ($pir_acc != "n/a")
{
echo "PIR record: | ";
echo "$PID_link |
\n";
}
#$reference_sql = "select pubmed,authors,title,journal from reference where gi=$ref_gi ";#good oct2709
$reference_sql = "select pubmed,authors,title,journal from reference where seq_id=$seqID ";#testing oct2709
$reference = FetchFromGOBASE($reference_sql, 1 );
$row = pg_fetch_row( $reference );
if ($row[0] or $row[2] ){
//$odd = ($odd==1)? 0 : 1;
//$bgcolor = ($odd==1) ? "#ddddff" : "#D3DCE3";
//echo " |
\n";
echo "Literature Reference |
\n";
//echo " |
\n";
if ($row[0]){
$odd = ($odd==1)? 0 : 1;
$bgcolor = ($odd==1) ? "#ddddff" : "#D3DCE3";
echo "Pubmed | $row[0] |
";
}
if ($row[2]){
$odd = ($odd==1)? 0 : 1;
$bgcolor = ($odd==1) ? "#ddddff" : "#D3DCE3";
echo "Title | $row[2] |
";
}
if ($row[1]){
$odd = ($odd==1)? 0 : 1;
$bgcolor = ($odd==1) ? "#ddddff" : "#D3DCE3";
echo "Authors | $row[1] |
";
}
if ($row[3]){
$odd = ($odd==1)? 0 : 1;
$bgcolor = ($odd==1) ? "#ddddfd" : "#D3DCEf";
echo "Journal | $row[3] |
";
}
}
echo "
\n";
echo "";
echo "
\n";
echo "";
// echo "
\n";
// echo "Species Name: | \n";
// echo " $spname_anchor | \n";
// echo "
\n";
// Annotated Genes
$result = FetchFromGOBASE( "select f_id, gene_name from extgene where " .
"seq_id= $seqID ",1 );
$flag = 0;
$count = 0;
$total = 0;
while( $row = pg_fetch_row( $result ) )
{
if($flag == 0)
{
echo "\n";
echo "Annotated Genes |
\n";
echo "
\n";
echo "\n";
echo "
\n";
$flag = 1;
}
if( $count == 0 ) echo "\n";
echo " $row[1] | \n";
$count++;
if( $count >=5 )
{
echo "
\n";
$count = 0;
}
$total ++;
}
if( $count != 0 )
{
while( $count < 5 )
{
echo " | \n";
$count++;
}
echo "\n";
}
if($flag == 1)
echo "
\n";
echo "";
// Annotated Introns
$result = FetchFromGOBASE( "select f_id from extintron where " .
"gi=$GI", 1 );#wol feb2010
$flag = 0;
$count = 0;
$total = 0;
while( $row = pg_fetch_row( $result ) )
{
if($flag == 0)
{
echo "
\n";
echo "Annotated Introns |
\n";
echo "
\n";
echo "\n";
echo "
\n";
$flag = 1;
}
if( $count == 0 ) echo "\n";
echo " $row[0] | \n";
$count++;
if( $count ==5 )
{
echo "
\n";
$count = 0;
}
$total++;
}
if( $count != 0 )
{
while( $count < 5 )
{
echo " | \n";
$count++;
}
echo "\n";
}
// if( $total == 0 )
// {
// echo "Not found. |
\n";
// }
if($flag == 1)
echo "
\n";
echo "";
// Annotated Exons
$result = FetchFromGOBASE( "select f_id from extexon where " .
"gi=$GI", 1 );#wol feb2010
$flag = 0;
$count = 0;
$total = 0;
while( $row = pg_fetch_row( $result ) )
{
if($flag == 0)
{
echo "
\n";
echo "Annotated Exons |
\n";
echo "
\n";
echo "\n";
echo "
\n";
$flag = 1;
}
if( $count == 0 ) echo "\n";
echo " $row[0] | \n";
$count++;
if( $count ==5 )
{
echo "
\n";
$count = 0;
}
$total++;
}
if( $count != 0 )
{
while( $count < 5 )
{
echo " | \n";
$count++;
}
echo "\n";
}
if($flag ==1)
echo "
\n";
echo "";
// Annotated RNA's
// Taxonomic Information
DisplayTaxonHits($tax_id);
include( "../common/footer.php" );
echo "