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 id='mainWLS' 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>
<?php $selectedDB[$dbid] = ' SELECTED';?>
<I>Arabidopsis</I> Genome Assembly
<SELECT NAME="dbid2" onchange="changeVersion();" style="font-size:10; color:#FF0000">
<?php
for($x=0;$x<sizeof($DBver);$x++){
echo " <OPTION $selectedDB[$x] VALUE=\"$x\">" . $DBver[$x][DBtag] . "</OPTION>\n";
}
?>
</SELECT><BR>
<P align='left'>
<B>Data Sets</B><BR><BR>
<?php
// if($dbid==0){
// echo "<U>Genomic Sequences :</U><BR>";
// echo "The five chromosomal sequences of <I>Arabidopsis thaliana</I> (cultivar: Columbia) were obtained from <A href=\"http://www.ncbi.nih.gov/Genbank/GenbankOverview.html\">GenBank</A> as accessions:";
// echo "<BR> <A href=\"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nucleotide&cmd=retrieve&list_uids=22330780\">NC_003070</A> (chromosome I, dated 8-20-2002, 30,028,691 bp)";
// echo "<BR> <A href=\"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nucleotide&cmd=retrieve&list_uids=22326553\">NC_003071</A> (chromosome II, dated 8-20-2002, 19,646,746 bp)";
// echo "<BR> <A href=\"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nucleotide&cmd=retrieve&list_uids=22331929\">NC_003074</A> (chromosome III, dated 8-20-2002, 23,467,821 bp)";
// echo "<BR> <A href=\"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nucleotide&cmd=retrieve&list_uids=22329272\">NC_003075</A> (chromosome IV, dated 8-20-2002, 17,550,036 bp)";
// echo "<BR> <A href=\"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nucleotide&cmd=retrieve&list_uids=22328163\">NC_003076</A> (chromosome V, dated 8-20-2002, 26,583,670 bp).";
// echo "<BR><BR>";
// echo "<U>EST Sequences :</U><BR>";
// echo "<I>Arabidopsis</I> ESTs were downloaded from NCBI's <A href=\"http://www.ncbi.nlm.nih.gov/dbEST/\">dbEST</A> database. Our analysis was based on 176,915 EST records (data set label: <A href=\"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nucleotide&cmd=search&term=Arabidopsis%5BORGN%5D+gbdiv_est%5BPROP%5D+1900%3A2002%2F10%5BPDAT%5D\">ATest</A>, version: October 25, 2002). ";
// echo "<BR><BR>";
// echo "<U>Protein Sequences :</U><BR>";
// echo "A data set of 27,288 putative <I>Arabidopsis</I> proteins was obtained from The Institute for Genome Research (<A href=\"http://www.tigr.org\">TIGR</A>). This data set is consistent with version 3.0 annotation of the GenBank release of the genome (data set label: <A href=\"ftp://ftp.tigr.org/pub/data/a_thaliana/ath1/SEQUENCES/ATH1.pep.gz\">ATpep</A>, version: October 24, 2002). ";
// echo "<BR><BR>";
// echo "<U>cDNA Sequences :</U><BR>";
// echo "The data set of 26,961 <I>A. thaliana</I> full-length cDNA sequences includes";
// echo "16,204 <a href=\"http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11910074&dopt=Abstract\">RAFL (Seki <I>et al.</I> (2002) Science 296, 141-145)</a>";
// echo "sequences and 5,000 <A href=\"ftp://ftp.tigr.org/pub/data/a_thaliana/ceres/CeresTigr\">Ceres-TIGR</A> sequences (available from the linked <A href=\"http://www.tigr.org\">TIGR</A> ftp site; version: March 2, 2001)";
// echo "as well as other sequences contributed to GenBank";
// echo "(data set label: <A href=\"/AtGDB/DATA/ATcdna\">ATcdna</A>; version: November 3, 2002).";
// echo "<BR><BR><BR>";
// }elseif($dbid==1){
// echo "<U>Genomic Sequences :</U><BR>";
// echo "The five chromosomal sequences of <I>Arabidopsis thaliana</I> (cultivar: Columbia) were obtained from <A href=\"http://www.ncbi.nih.gov/Genbank/GenbankOverview.html\">GenBank</A> as accessions:";
// echo "<BR> <A href=\"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nucleotide&cmd=retrieve&list_uids=30720142\">NC_003070</A> (chromosome I, dated 9-11-2003, 30,494,425 bp)";
// echo "<BR> <A href=\"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nucleotide&cmd=retrieve&list_uids=30698031\">NC_003071</A> (chromosome II, dated 9-11-2003, 19,705,359 bp)";
// echo "<BR> <A href=\"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nucleotide&cmd=retrieve&list_uids=30698537\">NC_003074</A> (chromosome III, dated 9-11-2003, 23,470,805 bp)";
// echo "<BR> <A href=\"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nucleotide&cmd=retrieve&list_uids=30698542\">NC_003075</A> (chromosome IV, dated 9-11-2003, 18,585,042 bp)";
// echo "<BR> <A href=\"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nucleotide&cmd=retrieve&list_uids=30698605\">NC_003076</A> (chromosome V, dated 9-11-2003, 26,992,728 bp).";
// echo "<BR><BR>";
// echo "<U>EST Sequences :</U><BR>";
// echo "<I>Arabidopsis</I> ESTs were downloaded from NCBI's <A href=\"http://www.ncbi.nlm.nih.gov/dbEST/\">dbEST</A> database. Our analysis was based on 191,244 EST records (data set label: <A href=\"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nucleotide&cmd=search&term=Arabidopsis%5BORGN%5D+gbdiv_est%5BPROP%5D+1900%3A2003%2F10%2F25%5BPDAT%5D\">ATest</A>, version: October 25, 2003). ";
// echo "<BR><BR>";
// echo "<U>Protein Sequences :</U><BR>";
// echo "A data set of 28,581 putative <I>Arabidopsis</I> proteins was obtained from The Institute for Genome Research (<A href=\"http://www.tigr.org\">TIGR</A>). This data set is consistent with the latest annotation of the GenBank release of the genome (data set label: <A href=\"ftp://ftp.tigr.org/pub/data/a_thaliana/ath1/SEQUENCES/ATH1.pep.gz\">ATpep</A>, version: September 11, 2003). ";
// echo "<BR><BR>";
// echo "<U>cDNA Sequences :</U><BR>";
// echo "The data set of 34,999 <I>A. thaliana</I> full-length cDNA sequences includes";
// echo "23,311 <a href=\"http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11910074&dopt=Abstract\">RAFL (Seki <I>et al.</I> (2002) Science 296, 141-145)</a>";
// echo "sequences and 5,000 <A href=\"ftp://ftp.tigr.org/pub/data/a_thaliana/ceres/CeresTigr\">Ceres-TIGR</A> sequences (available from the linked <A href=\"http://www.tigr.org\">TIGR</A> ftp site; version: March 2, 2001)";
// echo "as well as other sequences contributed to GenBank";
// echo "(data set label: <A href=\"/AtGDB/DATA/ATcdna\">ATcdna</A>; version: October 25, 2003).";
// echo "<BR><BR><BR>";
// }elseif($dbid==2){
echo "<U>Genomic Sequences :</U><BR>";
echo "The five chromosomal sequences of <I>Arabidopsis thaliana</I> (cultivar: Columbia) were obtained from <A href=\"http://www.ncbi.nih.gov/Genbank/GenbankOverview.html\">GenBank</A> as accessions:";
echo "<BR> <A href=\"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nucleotide&cmd=retrieve&list_uids=42592260\">NC_003070</A> (chromosome I, version 5, dated 1-25-2005, 30,432,563 bp)";
echo "<BR> <A href=\"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nucleotide&cmd=retrieve&list_uids=30698031\">NC_003071</A> (chromosome II, version 3, dated 8-3-2004, 19,705,359 bp)";
echo "<BR> <A href=\"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nucleotide&cmd=retrieve&list_uids=30698537\">NC_003074</A> (chromosome III, version 4, dated 8-6-2004, 23,470,805 bp)";
echo "<BR> <A href=\"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nucleotide&cmd=retrieve&list_uids=30698542\">NC_003075</A> (chromosome IV, version 3, dated 1-25-2004, 18,585,042 bp)";
echo "<BR> <A href=\"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nucleotide&cmd=retrieve&list_uids=30698605\">NC_003076</A> (chromosome V, version 4, dated 8-6-2004, 26,992,728 bp).";
echo "<BR> <A href=\"http://www.ncbi.nlm.nih.gov/entrez/sutils/girevhist.cgi?val=+NC_003070++NC_003071++NC_003074++NC_003075++NC_003076\">Genbank sequence history</A>";
echo "<BR><BR>";
echo "<U>Protein Sequences :</U><BR>";
echo "A data set of 28,952 putative <I>Arabidopsis</I> proteins was obtained from The Institute for Genome Research (<A href=\"http://www.tigr.org\">TIGR</A>). This data set is consistent with the latest annotation of the GenBank release of the genome (data set label: <A href=\"ftp://ftp.tigr.org/pub/data/a_thaliana/ath1/SEQUENCES/ATH1.pep.gz\">ATpep</A>, updated: Oct 3, 2004 [genome assembly version 5.0]). ";
echo "<BR><BR>";
echo "<U>EST Sequences :</U><BR>";
echo "<I>Arabidopsis</I> ESTs were downloaded from NCBI's <A href=\"http://www.ncbi.nlm.nih.gov/dbEST/\">dbEST</A> database. Our analysis was based on 418,564 EST records (data set label: <A href=\"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nucleotide&cmd=search&term=Arabidopsis%20thaliana%5BORGN%5D+gbdiv_est%5BPROP%5D+1900%3A2005%2F6%2F1%5BPDAT%5D\">ATest</A>, updated: May 1, 2005). ";
echo "<BR><BR>";
echo "<U>cDNA Sequences :</U><BR>";
echo "The data set of 64,840 <I>A. thaliana</I> full-length cDNA sequences includes:<BR>";
echo "27,104 <a href=\"http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11910074&dopt=Abstract\">RAFL (Seki <I>et al.</I> (2002) Science 296: 141-145)</a> sequences<BR>";
echo "21,503 <a href=\"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14993207\">GSLT (Castelli <I>et al.</I> (2004) Genome Research 14:406)</a> sequences<BR>";
echo "5,000 <A href=\"ftp://ftp.tigr.org/pub/data/a_thaliana/ceres/CeresTigr\">Ceres-TIGR</A> sequences (available from the linked <A href=\"http://www.tigr.org\">TIGR</A> ftp site; version: March 2, 2001)<BR> ";
echo "as well as other sequences contributed to GenBank ";
echo "(data set label: ATcdna; updated: May 1, 2005).";
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