Show resource.php syntax highlighted
<?php
if(empty($SITEDEF_H)){require('SITEDEF.php');}
if(empty($PARAM_H)){require('getPARAM.php');}
require('SSI_GDBprep.php');
virtual("${CGIPATH}SSI_GDBgui.pl/TWO_COLUMN_HEADER/" . $SSI_QUERYSTRING);
?>
<div align="center">
<H2>Data Sets, Methods, and Resources</H2>
<P align='left'>
<?php echo $SITENAMEshort; ?> encompasses primary sequence data obtained from GenBank, including the most current
gss and BAC assembly and annotation, EST and cDNA sequences, and protein sequences derived from
the annotated genes.
<?php echo $LATINORGN; ?> genome assemblies refer to the pseudo-chromosome tiling of individual genomic sequence
fragments obtained from the listed assembly sources.
The mapping of cDNA and EST sequences onto the genome as well as interpretations of the overall
data are based on our own spliced alignment results.
</P>
<P align='left'>
The <?php echo $COMMONORGN2; ?> genome assembly is still being refined and completed.
<?php echo $SITENAMEshort; ?> attempts to remain synchronized with the most recent release of the
genome assembly and annotations.
</P>
Zea mays BAC Genome
<?php $selectedDB[$cgi_paramHR[dbid]] = 'SELECTED';?>
<SELECT NAME="dbid0" onchange="changeVersion();" style="font-size:10; color:#FF0000">
<?php
for($x=0;$x<sizeof($DBver);$x++){
$ASMBLY = $DBver[$x][DBtag];
echo " <OPTION $selectedDB[$x] VALUE=\"$x\">$ASMBLY</OPTION>\n";
}
?>
</SELECT><BR>
<P align='left'>
<B>Data Sets</B><BR><BR>
<?php
//if($cgi_paramHR[dbid]==1){
echo "<U>BAC Genomic Sequences :</U><BR>";
echo "24 Maize complete BAC sequences Sequences were obtained from <A href=\"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=nucleotide&term=%22Zea%20mays%22%5BORGN%5D+%22complete%20sequence%22%5BTITL%5D+1900%3A2005%2F02%2F1%5BPDAT%5D+BAC\">NCBI</A> as of February 1, 2005.<BR>";
echo "The 464 maize unfinished BAC sequences were obtained from <A href=\"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=nucleotide&term=%22Zea%20mays%22%5BORGN%5D+HTG%5BPROP%5D+1900%3A2005%2F02%2F1%5BPDAT%5D\">NCBI HTG repository</A>.";
echo "<BR><BR>";
echo "<U>EST Sequences :</U><BR>";
echo "Maize ESTs were downloaded from NCBI's <A href=\"http://www.ncbi.nlm.nih.gov/dbEST/\">dbEST</A> database. Our analysis was based on 417,803 EST records (data set label: <A href=\"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nucleotide&cmd=search&term=%22Zea%20mays%22%5BORGN%5D+gbdiv_est%5BPROP%5D+1900%3A2005%2F2%2F1%5BPDAT%5D\">ZMest</A>, version: February 1, 2005). ";
echo "<BR><BR>";
echo "<U>cDNA Sequences :</U><BR>";
echo "The data set of 3,160 <I>Z. mays</I> full-length cDNA sequences was obtained from Genbank ";
echo "(data set label: <A href=\"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nucleotide&cmd=search&term=%22Zea%20mays%22%5BORGN%5D+fli_cdna%5Bkeyword%5D+1900%3A2005%2F2%2F1%5BPDAT%5D\">ZMcdna</A>; version: February 1, 2005).";
echo "<BR><BR><BR>";
/*}elseif($cgi_paramHR[dbid]==0){
echo "<U>Genomic Sequences :</U><BR>";
echo "3,285 Rice Genomic Sequences were obtained from <A href=\"http://rgp.dna.affrc.go.jp/cgi-bin/statusdb/irgsp-status.cgi\">the International Rice Genome Sequencing project</A>";
echo " (data set label: OSgseg; version: Jan 1, 2004).<BR>";
echo "The assembly of the twelve chromosome sequences of <I>Oryza sativa</I> (ie the placement of BACs relative to one another) were obtained from <A href=\"http://www.tigr.org/tdb/e2k1/osa1/pseudomolecules/info.shtml\">the TIGR rice genome website</A>.";
echo "<BR><BR>";
echo "<U>EST Sequences :</U><BR>";
echo "Rice ESTs were downloaded from NCBI's <A href=\"http://www.ncbi.nlm.nih.gov/dbEST/\">dbEST</A> database. Our analysis was based on 266,004 EST records (data set label: <A href=\"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nucleotide&cmd=search&term=Rice%5BORGN%5D+gbdiv_est%5BPROP%5D+1900%3A2004%2F1%5BPDAT%5D\">OSest</A>, version: Jan 1, 2004). ";
echo "<BR><BR>";
echo "<U>cDNA Sequences :</U><BR>";
echo "The data set of 32,128 <I>O. sativa</I> full-length cDNA sequences was obtained from <A href=\"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nucleotide&cmd=search&term=Rice%5BORGN%5D+fli_cdna%5Bkeyword%5D+1900%3A2004%2F1%5BPDAT%5D\">Genbank</A>";
echo " (data set label: <A href=\"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nucleotide&cmd=search&term=Rice%5BORGN%5D+fli_cdna%5Bkeyword%5D+1900%3A2004%2F1%5BPDAT%5D\">OScdna</A>; version: Jan 1, 2004).";
echo "<BR><BR><BR>";
}*/
?>
</P>
<P align='left'>
<B>Methods</B><BR><BR>
<A href="http://bioinformatics.iastate.edu/cgi-bin/gs.cgi">GeneSeqer</A><BR>
GeneSeqer is a gene identification tool based on spliced alignment or "spliced threading" of cDNAs/ESTs into a genomic DNA sequence template.
<BR><BR><BR>
</P>
<P align='left'>
<B>Resources</B><BR><BR>
<A href="http://www.ncbi.nlm.nih.gov/BLAST/">NCBI BLAST</A><BR>
Stand-alone (local) BLAST is a pairwise alignment search tool used for sequence-based querying of on-site databases.
<BR><BR>
<A href="http://www.mysql.com">MySQL</A><BR>
MySQL is "the world's most popular Open Source Database, designed for speed, power and precision in mission critical, heavy load use."
<BR><BR>
<A href="http://httpd.apache.org/">Apache</A><BR>
The Apache HTTP Server Project is "an effort to develop and maintain an open-source HTTP server for modern operating systems including UNIX and Windows NT. Apache has been the most popular web server on the Internet since April of 1996."
<BR><BR>
<A href="http://bookmarks.cpan.org/">Perl</A><BR>
A web site without it just isn't a web site at all!
<BR><BR>
<A href="http://stein.cshl.org/WWW/CGI/">Perl::CGI.pm</A><BR>
This perl 5 library "uses objects to create Web fill-out forms on the fly and to parse their contents. It provides a
simple interface for parsing and interpreting query strings passed to CGI scripts. However, it also offers a rich
set of functions for creating fill-out forms. Instead of remembering the syntax for HTML form elements, you
just make a series of perl function calls. An important fringe benefit of this is that the value of the previous
query is used to initialize the form, so that the state of the form is preserved from invocation to invocation."
<BR><BR>
<A href="http://stein.cshl.org/WWW/software/GD/">Perl::GD.pm</A><BR>
Graphics on-the-fly just wouldn't be the same without it!
</div>
<?php
require('SSI_GDBprep.php');
virtual("${CGIPATH}SSI_GDBgui.pl/STANDARD_FOOTER/" . $SSI_QUERYSTRING);
?>
See more files for this project here