#!/usr/bin/perl -w
$PROCESS_INPUT_URL = 'search_holdingClone_results.cgi';
#$CGI_VERSION = "(search_holdingClone.cgi v 0.1 beta 1a)";
BEGIN{
print "Content-type: text/html\n\n";
# Ensure that errors go to the web browser.
open(STDERR, ">&STDOUT");
$| = 1;
print '';
}
use Carp;
use CGI;
# The CGI module is available from
# http://www.genome.wi.mit.edu/ftp/distribution/software/WWW/
main();
sub main {
$LIGHT_COLOR="#BBFFBB";
$C_ROW = "<tr bgcolor=$LIGHT_COLOR>";
#$OLIGO_INPUT_SIZE=30;
#$SOURCE_SEQUENCE_WIDTH = 3 * ($OLIGO_INPUT_SIZE + 1) + 2;
#$INPUT_VALUE = "";
$query = new CGI;
input_screen($query);
}
sub input_screen {
my ($query) = @_;
my $script = "function clearAll() {\n";
$script .= " document.data.ACCESSION_CHECK.checked = false;\n";
$script .= " document.data.RIKEN_CHECK.checked = false;\n";
$script .= " document.data.TUID_CHECK.checked = false;\n";
$script .= " document.data.RELATED_CHECK.checked = false;\n";
$script .= " document.data.GENE_CHECK.checked = false;\n";
$script .= " document.data.GENEID_CHECK.checked = false;\n";
$script .= " document.data.PROTEIN_CHECK.checked = false;\n";
$script .= " document.data.UNIGENE_CHECK.checked = false;\n";
$script .= "}\n";
print $query->start_html(-title => "Search HoldingClone",
-script => $script);
print qq{
<form name="data"
action="$PROCESS_INPUT_URL"
method="post"
enctype="x-www-form-urlencoded">
<table border=0 width="100%">
$C_ROW
<td rowspan=2> <font size="+3"> Search holdingClone </font> <br>
</table>
<br>
input search word<br>
<input type="text" class="box" name="INPUT_TEXT" size="80">
<input type="radio" name="SEARCH_FLG" value=1> and
<input type="radio" name="SEARCH_FLG" value=0 checked> or
<br>
"You can use multiple search words with using space."
<br><br>
<input type="radio" name="HUMAN_FLG" value=1 checked> Human clone
<input type="radio" name="HUMAN_FLG" value=0> Mouse FANTOM3 clone set
<br><br>
check the target for search<br>
<input type="checkbox" name="ACCESSION_CHECK" value=1 checked>accession
<input type="checkbox" name="RIKEN_CHECK" value=1 checked>RIKEN_cloneid
<input type="checkbox" name="TUID_CHECK" value=1 checked>TUID
<input type="checkbox" name="RELATED_CHECK" value=1 checked>Related_TUID
<input type="checkbox" name="GENE_CHECK" value=1 checked>gene
<input type="checkbox" name="GENEID_CHECK" value=1 checked>GeneID
<input type="checkbox" name="PROTEIN_CHECK" value=1 checked>protein_id
<input type="checkbox" name="UNIGENE_CHECK" value=1 checked>unigene_id
<br>
<input type="button" onClick="clearAll()" value="clear check"><br>
<input type="reset" value="reset"><br>
<br>
<input type="submit" name=" Go! " value=" Go! ">
<br>
</form>
<pre>
<br>
<b>About 'status' columun.</b>
[Status values for full length sequence]
<b>"OK"</b> : Same sequence as RefSeq. <b><font color="red">Good!</font></b>
<b>"C"</b> : Complete CDS as RefSeq. <b><font color="red">Good!</font></b>
"Cs" : Complete CDS as RefSeq with substitution.
"Cg" : Complete CDS as RefSeq with insertion and/or deletion.
"Cgs" : Complete CDS as RefSeq with ins/del and substitusion.
"Cfs" : Complete CDS as RefSeq with frame shift.
"P" : Partial CDS as RefSeq.
"Ps" : Partial CDS as RefSeq with subsititution.
"Pg" : Partial CDS as RefSeq with insertion and/or deletion.
"Pgs" : Partial CDS as RefSeq with ins/del and sub.
"Pfs" : Partial CDS as RefSeq with frame shift.
"Pfs" : Partial with (frame shift)
[Status values for 5' and/or 3' end sequences]
"5-longer:3-longer" : 5'-end and 3'-end sequences are mapped on genome sequences
and both ends are longer than longest transcript on TU.
"5-longer:3-shoter" : (Same as above ) and 3-end is shorter than than longest transcript on TU.
"5-longer:na" : 5'-end sequences are mapped on genome sequences but not 3'-end
and both 5'-ends are longer than longest transcript on TU.
"5-shorter:3-longer" : (Same logics as above.)
"5-shorter:3-shorter" : (Same logics as above.)
"5-shorter:na" : (Same logics as above.)
<b>About 'seq_verify' columun.</b>
[Status values for sequencing verification (ID check sequence)]
<b>"verified"</b> : This clone was verified with sequencing and comparing with NCBI genbank's sequence of this clone. <b><font color="red">Good!</font></b>
"unverified" : This clone couldn't be verified because it couldn't found similality with NCBI genbanks's sequence.
"seq_lowQual" : This clone couldn't be verified because of low quality sequence. (It has possibility of contamination of clones and/or less quality of clone culturing.)
"nt_not_available" : This clone's NCBI genbank's sequence have been expired by clone distributer.
"seq_not-yet" : Sequencing verification of this clones have not done yet.
"no_growth" : This clone could not growth on well of plate. It might be low quality of clones.
"source" : Source clone. (Sequencing verification isn't necessarry.)
<b>About columns of alignment values between clone's nucleotide sequence and RefSeq peptide (fastx).</b>
"refseq_nuc" : Accession ID of refseq nucleotide.
"refseq_pep" : Accession ID of refseq peptide.
"refseq_status" : Please see document on NCBI RefSeq web site.(<a href="http://www.ncbi.nlm.nih.gov/RefSeq/key.html#status">here</a>)
"status" : See as above.
"ident" : Local identity value.
"gident : Global identity value. (There is gap if 'ident' and 'gident' are different.)
"overlap" : Overlapped length.
"q_len" : Length of clone's sequence.
"q_start" : Alignment start position of clone's sequence.
"q_stop" : Alignment stop position of clone's sequence.
"s_len" : Length of RefSeq peptide sequence.
"s_start" : Alignment start position of RefSeq peptide sequence.
"s_stop" : Alignment stop position of RefSeq peptide sequence.
</pre>
<H3>Data Download</H3>
<a href="./data"><b>List of Clones</b></a>
};
print $query->end_html;
print "\n";
}