vector.php from eXtensible Genome Data Broker at Krugle

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<?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">

<h1 align="center"><font color="#000000"><big>Vector Sequence Contaminations</big></font></h1>

   <P align="left">The latest assembly of the <I>Arabidopsis thaliana</I> genome (GenBank entries of 2/19/04) contains vector sequence contaminations.  For example, <a href=<?php echo"\"${CGIPATH}getRegion.pl?dbid=0&chr=2&l_pos=3610001&r_pos=3630000\""; ?>><font color="#0000FF">region 3,617,880 to 3,625,027 of chromosome II</font></a> is a cloning vector. Alignments were generated using VMATCH; see <a href="ATchr2.aln" target="blank"><font color="#0000FF">here</font></a> for the output.

<P style="text-align:left; margin:5px auto;">
Complete list of vector contaminations:
</P>
<TABLE BORDER="1" CELLSPACING="2" CELLPADDING="5">

<TR ALIGN="CENTER" VALIGN="BOTTOM">
<TD><B>CHROMOSOME</B></TD>
<TD><B>LOCATION</B></TD>
<TD><B>GENOMIC CONTEXT VIEW</B></TD>
<TD><B>vmatch ALIGNMENT</B></TD>
</TR>

<TR ALIGN="CENTER" VALIGN="BOTTOM">
<TD>2</TD>
<TD>3,617,880 to 3,625,027</TD>
<TD><a href=<?php echo"\"${CGIPATH}getRegion.pl?dbid=0&chr=2&l_pos=3610001&r_pos=3630000\""; ?> target="blank"><font color="#0000FF">gc-vc2</font></a></TD>
<TD><a href="ATchr2.aln" target="blank"><font color="#0000FF">vm-vc2</font></a></TD>
</TR>

<TR ALIGN="CENTER" VALIGN="BOTTOM">
<TD>3</TD>
<TD>5 to 101</TD>
<TD><a href=<?php echo"\"${CGIPATH}getRegion.pl?dbid=0&chr=3&l_pos=1&r_pos=1000\""; ?> target="blank"><font color="#0000FF">gc-vc3a</font></a></TD>
<TD><a href="ATchr3.aln" target="blank"><font color="#0000FF">vm-vc3</font></a></TD>
</TR>

<TR ALIGN="CENTER" VALIGN="BOTTOM">
<TD>3</TD>
<TD>13,748,162 to 13,748,842</TD>
<TD><a href=<?php echo"\"${CGIPATH}getRegion.pl?dbid=0&chr=3&l_pos=13740001&r_pos=13770000\""; ?> target="blank"><font color="#0000FF">gc-vc3b</font></a></TD>
<TD><a href="ATchr3.aln" target="blank"><font color="#0000FF">vm-vc3</font></a></TD>
</TR>

<TR ALIGN="CENTER" VALIGN="BOTTOM">
<TD>3</TD>
<TD>13,754,115 to 13,760,806</TD>
<TD><a href=<?php echo"\"${CGIPATH}getRegion.pl?dbid=0&chr=3&l_pos=13740001&r_pos=13770000\""; ?> target="blank"><font color="#0000FF">gc-vc3c</font></a></TD>
<TD><a href="ATchr3.aln" target="blank"><font color="#0000FF">vm-vc3</font></a></TD>
</TR>

<TR ALIGN="CENTER" VALIGN="BOTTOM">
<TD>5</TD>
<TD>11,246,005 to 11,246,090</TD>
<TD><a href=<?php echo"\"${CGIPATH}getRegion.pl?dbid=0&chr=5&l_pos=11245001&r_pos=11247000\""; ?> target="blank"><font color="#0000FF">gc-vc5</font></a></TD>
<TD><a href="ATchr5.aln" target="blank"><font color="#0000FF">vm-vc5</font></a></TD>
</TR>

</TABLE>

<ul>
  <li> <h4 align="left"><a href="http://www.ncbi.nlm.nih.gov/VecScreen/UniVec.html" target="blank"><font color="#0000FF">NCBI UniVec</font></a> - database and tools "that can be used to quickly identify segments within nucleic acid sequences which may be of vector origin (vector contamination)"</h4>

  <li> <h4 align="left"><a href="http://www.vmatch.de/" target="blank"><font color="#0000FF">VMATCH</font></a> - powerful string matching software developed by Dr. Stefan Kurtz</h4>
</ul>


</div>

<?php
require('SSI_GDBprep.php');
virtual("${CGIPATH}SSI_GDBgui.pl/STANDARD_FOOTER/" . $SSI_QUERYSTRING);
?>

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eXtensible Genome Data Broker

The xGDB project provides scientists with an online portal for the integration of diverse sources of genomic data. Portals allow researchers to effectively target a specific scientific question by customizing their interactions with available data.

Project homepage: http://sourceforge.net/projects/xgdb
Programming language(s): JavaScript,Perl,PHP
License: other

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  ATchr2.aln
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  vector.php