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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<title>Comparative applications</title>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<style type="text/css">
<!--
body {
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h2 {
	background-color: #BBBBFF;
	font-style: italic;
}
h3 {
	background-color: #CDCDEE;
}
h4 {
	background-color: #EFEFEF;
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code {
	color: #CC0000;
}
td {
	vertical-align: top;
}
.centered {
	text-align: center;
}
.right {
	text-align: right;
}
-->
</style>
</head>
<body>
<h3>Published genomes suitable for whole genome comparison</h3>
<p>The MUMmer package provides efficient means for comparing an entire genome 
  against another. However, until 1999 there were no two genomes of sufficient 
  similarity to compare. With the publication of the second strain of <em>Helicobacter 
  pylori</em> in 1999, following the publication of the first strain in 1997, 
  the scientific world had its first chance to look at two complete bacterial 
  genomes whose DNA sequences were highly similar. The number of pairs of closely-related 
  genomes has exploded in recent years, facilitating many comparative studies. 
  For instance, the published databases include the following genomes for which 
  multiple strains and/or multiple species have been sequenced:</p>
<div class="centered"> 
  <table width="60%" border="0">
    <tr> 
      <td nowrap> <h5>multiple strains of...</h5>
        <ul>
          <li><em>Agrobacterium tumefaciens</em></li>
          <li><em>Bacillus anthracis</em></li>
          <li><em>Brucella melitensis</em></li>
          <li><em>Buchnera aphidicola</em></li>
          <li><em>Chlamydophila pneumoniae</em></li>
          <li><em>Escherichia coli</em></li>
          <li><em>Helicobacter pylori</em></li>
          <li><em>Mycobacterium tuberculosis</em></li>
          <li><em>Neisseria meningitidis</em></li>
          <li><em>Staphylococcus aureus</em></li>
          <li><em>Streptococcus pyogenes</em></li>
          <li><em>Streptococcus pneumoniae</em></li>
          <li><em>Yersinia pestis</em></li>
        </ul></td>
      <td nowrap> <h5>multiple species of...</h5>
        <ul>
          <li><em>Bacillus</em></li>
          <li><em>Chlamydia</em></li>
          <li><em>Clostridium</em></li>
          <li><em>Corynebacterium</em></li>
          <li><em>Lactobacillus</em></li>
          <li><em>Listeria</em></li>
          <li><em>Methanosarcina</em></li>
          <li><em>Mycobacterium</em></li>
          <li><em>Mycoplasma</em></li>
          <li><em>Plasmodium</em></li>
          <li><em>Pseudomonas</em></li>
          <li><em>Pyrococcus</em></li>
          <li><em>Rickettsia</em></li>
          <li><em>Saccharomyces</em></li>
          <li><em>Staphylococcus</em></li>
          <li><em>Streptococcus</em></li>
          <li><em>Thermoplasma</em></li>
          <li><em>Vibrio</em></li>
          <li><em>Xanthomonas</em></li>
          <li><em>Xylella</em></li>
        </ul></td>
    </tr>
  </table>
</div>
<p>Most of these genomes can be obtained from the NCBI ftp site: <a href="ftp://ftp.ncbi.nlm.nih.gov/genomes/">ftp://ftp.ncbi.nlm.nih.gov/genomes/</a></p>
<h3>Timing analysis for the whole genome alignment of Human vs. Human</h3>
<p>With the capability to align the entire human genome to itself, there is no 
  genome too large for MUMmer. The following table gives run times and space requirements 
  for a cross comparison of all human chromosomes. The 1st column indicates the 
  chromosome number, with &quot;Un&quot; referring to unmapped contigs. Column 
  2 shows chromosome length and column 4 shows the length of the total genomic 
  DNA searched against the chromosome in column 1. Column 3 shows the time to 
  construct the suffix tree, and column 5 the time to stream the query sequence 
  through it. Column 6 shows the maximum amount of computer memory occupied by 
  the program and data, and column 7 shows memory usage for the suffix tree in 
  bytes per base pair. Each human chromosome was used as a reference, and the 
  rest of the genome was used as a query and streamed against it. To avoid duplication, 
  we only included chromosomes in the query if they had not already been compared; 
  thus we first used chromosome 1 as a reference, and streamed the other 23 chromosomes 
  against it. Then we used chromosome 2 as a reference, and streamed chromosomes 
  3&#8211;22, X, and Y against that, and so on.</p>
<div class="centered"> 
  <table border="0" cellpadding="1" cellspacing="3">
    <tr align="right"> 
      <td bgcolor="#EFEFEF"><strong><font size="2">Chr </font></strong></td>
      <td bgcolor="#EFEFEF"><strong><font size="2">Ref length<br>
        (Mbp)</font></strong></td>
      <td bgcolor="#EFEFEF"><strong><font size="2">Suffix time<br>
        (min)</font></strong></td>
      <td bgcolor="#EFEFEF"><strong><font size="2">Qry length<br>
        (Mbp)</font></strong></td>
      <td bgcolor="#EFEFEF"><strong><font size="2">Query time<br>
        (min)</font></strong></td>
      <td bgcolor="#EFEFEF"><strong><font size="2">Total space</font><font size="2"><br>
        (Mb)</font></strong></td>
      <td bgcolor="#EFEFEF"><strong><font size="2">Suffix space<br>
        (bytes/bp)</font></strong></td>
    </tr>
    <tr align="right"> 
      <td bgcolor="#E6E6FA"><font size="2">1 </font></td>
      <td bgcolor="#E6E6FA"><font size="2">221.8</font></td>
      <td bgcolor="#E6E6FA"><font size="2">24.6</font></td>
      <td bgcolor="#E6E6FA"><font size="2">2617.1</font></td>
      <td bgcolor="#E6E6FA"><font size="2">679.5</font></td>
      <td bgcolor="#E6E6FA"><font size="2">3702</font></td>
      <td bgcolor="#E6E6FA"><font size="2">15.43</font></td>
    </tr>
    <tr align="right"> 
      <td bgcolor="#E6E6FA"><font size="2">2</font></td>
      <td bgcolor="#E6E6FA"><font size="2">237.6</font></td>
      <td bgcolor="#E6E6FA"><font size="2">27.4</font></td>
      <td bgcolor="#E6E6FA"><font size="2">2379.5</font></td>
      <td bgcolor="#E6E6FA"><font size="2">625.8</font></td>
      <td bgcolor="#E6E6FA"><font size="2">3908</font></td>
      <td bgcolor="#E6E6FA"><font size="2">15.43</font></td>
    </tr>
    <tr align="right"> 
      <td bgcolor="#E6E6FA"><font size="2">3</font></td>
      <td bgcolor="#E6E6FA"><font size="2">194.8</font></td>
      <td bgcolor="#E6E6FA"><font size="2">21.2</font></td>
      <td bgcolor="#E6E6FA"><font size="2">2184.7</font></td>
      <td bgcolor="#E6E6FA"><font size="2">565.0</font></td>
      <td bgcolor="#E6E6FA"><font size="2">3232</font></td>
      <td bgcolor="#E6E6FA"><font size="2">15.43</font></td>
    </tr>
    <tr align="right"> 
      <td bgcolor="#E6E6FA"><font size="2">4</font></td>
      <td bgcolor="#E6E6FA"><font size="2">188.4</font></td>
      <td bgcolor="#E6E6FA"><font size="2">22.4</font></td>
      <td bgcolor="#E6E6FA"><font size="2">1996.3</font></td>
      <td bgcolor="#E6E6FA"><font size="2">518.0</font></td>
      <td bgcolor="#E6E6FA"><font size="2">3121</font></td>
      <td bgcolor="#E6E6FA"><font size="2">15.43</font></td>
    </tr>
    <tr align="right"> 
      <td bgcolor="#E6E6FA"><font size="2">5</font></td>
      <td bgcolor="#E6E6FA"><font size="2">177.7</font></td>
      <td bgcolor="#E6E6FA"><font size="2">18.6</font></td>
      <td bgcolor="#E6E6FA"><font size="2">1818.6</font></td>
      <td bgcolor="#E6E6FA"><font size="2">461.4</font></td>
      <td bgcolor="#E6E6FA"><font size="2">2952</font></td>
      <td bgcolor="#E6E6FA"><font size="2">15.43</font></td>
    </tr>
    <tr align="right"> 
      <td bgcolor="#E6E6FA"><font size="2">6</font></td>
      <td bgcolor="#E6E6FA"><font size="2">175.8</font></td>
      <td bgcolor="#E6E6FA"><font size="2">17.9</font></td>
      <td bgcolor="#E6E6FA"><font size="2">1642.8</font></td>
      <td bgcolor="#E6E6FA"><font size="2">407.6</font></td>
      <td bgcolor="#E6E6FA"><font size="2">2900</font></td>
      <td bgcolor="#E6E6FA"><font size="2">15.43</font></td>
    </tr>
    <tr align="right"> 
      <td bgcolor="#E6E6FA"><font size="2">7</font></td>
      <td bgcolor="#E6E6FA"><font size="2">153.8</font></td>
      <td bgcolor="#E6E6FA"><font size="2">15.7</font></td>
      <td bgcolor="#E6E6FA"><font size="2">1489.0</font></td>
      <td bgcolor="#E6E6FA"><font size="2">360.1</font></td>
      <td bgcolor="#E6E6FA"><font size="2">2550</font></td>
      <td bgcolor="#E6E6FA"><font size="2">15.43</font></td>
    </tr>
    <tr align="right"> 
      <td bgcolor="#E6E6FA"><font size="2">8</font></td>
      <td bgcolor="#E6E6FA"><font size="2">142.8</font></td>
      <td bgcolor="#E6E6FA"><font size="2">14.4</font></td>
      <td bgcolor="#E6E6FA"><font size="2">1346.2</font></td>
      <td bgcolor="#E6E6FA"><font size="2">322.3</font></td>
      <td bgcolor="#E6E6FA"><font size="2">2378</font></td>
      <td bgcolor="#E6E6FA"><font size="2">15.43</font></td>
    </tr>
    <tr align="right"> 
      <td bgcolor="#E6E6FA"><font size="2">9</font></td>
      <td bgcolor="#E6E6FA"><font size="2">117.0</font></td>
      <td bgcolor="#E6E6FA"><font size="2">10.7</font></td>
      <td bgcolor="#E6E6FA"><font size="2">1229.2</font></td>
      <td bgcolor="#E6E6FA"><font size="2">303.7</font></td>
      <td bgcolor="#E6E6FA"><font size="2">1974</font></td>
      <td bgcolor="#E6E6FA"><font size="2">15.43</font></td>
    </tr>
    <tr align="right"> 
      <td bgcolor="#E6E6FA"><font size="2">10</font></td>
      <td bgcolor="#E6E6FA"><font size="2">131.1</font></td>
      <td bgcolor="#E6E6FA"><font size="2">13.2</font></td>
      <td bgcolor="#E6E6FA"><font size="2">1098.1</font></td>
      <td bgcolor="#E6E6FA"><font size="2">263.3</font></td>
      <td bgcolor="#E6E6FA"><font size="2">2195</font></td>
      <td bgcolor="#E6E6FA"><font size="2">15.43</font></td>
    </tr>
    <tr align="right"> 
      <td bgcolor="#E6E6FA"><font size="2">11</font></td>
      <td bgcolor="#E6E6FA"><font size="2">133.2</font></td>
      <td bgcolor="#E6E6FA"><font size="2">13.1</font></td>
      <td bgcolor="#E6E6FA"><font size="2">964.9</font></td>
      <td bgcolor="#E6E6FA"><font size="2">225.6</font></td>
      <td bgcolor="#E6E6FA"><font size="2">2228</font></td>
      <td bgcolor="#E6E6FA"><font size="2">15.43</font></td>
    </tr>
    <tr align="right"> 
      <td bgcolor="#E6E6FA"><font size="2">12</font></td>
      <td bgcolor="#E6E6FA"><font size="2">129.4</font></td>
      <td bgcolor="#E6E6FA"><font size="2">12.5</font></td>
      <td bgcolor="#E6E6FA"><font size="2">835.5</font></td>
      <td bgcolor="#E6E6FA"><font size="2">195.9</font></td>
      <td bgcolor="#E6E6FA"><font size="2">2168</font></td>
      <td bgcolor="#E6E6FA"><font size="2">15.43</font></td>
    </tr>
    <tr align="right"> 
      <td bgcolor="#E6E6FA"><font size="2">13</font></td>
      <td bgcolor="#E6E6FA"><font size="2">95.2</font></td>
      <td bgcolor="#E6E6FA"><font size="2">8.6</font></td>
      <td bgcolor="#E6E6FA"><font size="2">740.3</font></td>
      <td bgcolor="#E6E6FA"><font size="2">163.6</font></td>
      <td bgcolor="#E6E6FA"><font size="2">1633</font></td>
      <td bgcolor="#E6E6FA"><font size="2">15.44</font></td>
    </tr>
    <tr align="right"> 
      <td bgcolor="#E6E6FA"><font size="2">14</font></td>
      <td bgcolor="#E6E6FA"><font size="2">88.2</font></td>
      <td bgcolor="#E6E6FA"><font size="2">7.5</font></td>
      <td bgcolor="#E6E6FA"><font size="2">652.1</font></td>
      <td bgcolor="#E6E6FA"><font size="2">141.0</font></td>
      <td bgcolor="#E6E6FA"><font size="2">1523</font></td>
      <td bgcolor="#E6E6FA"><font size="2">15.44</font></td>
    </tr>
    <tr align="right"> 
      <td bgcolor="#E6E6FA"><font size="2">15</font></td>
      <td bgcolor="#E6E6FA"><font size="2">83.6</font></td>
      <td bgcolor="#E6E6FA"><font size="2">6.8</font></td>
      <td bgcolor="#E6E6FA"><font size="2">568.5</font></td>
      <td bgcolor="#E6E6FA"><font size="2">122.1</font></td>
      <td bgcolor="#E6E6FA"><font size="2">1451</font></td>
      <td bgcolor="#E6E6FA"><font size="2">15.44</font></td>
    </tr>
    <tr align="right"> 
      <td bgcolor="#E6E6FA"><font size="2">16</font></td>
      <td bgcolor="#E6E6FA"><font size="2">80.9</font></td>
      <td bgcolor="#E6E6FA"><font size="2">6.4</font></td>
      <td bgcolor="#E6E6FA"><font size="2">487.6</font></td>
      <td bgcolor="#E6E6FA"><font size="2">106.3</font></td>
      <td bgcolor="#E6E6FA"><font size="2">1409</font></td>
      <td bgcolor="#E6E6FA"><font size="2">15.44</font></td>
    </tr>
    <tr align="right"> 
      <td bgcolor="#E6E6FA"><font size="2">17</font></td>
      <td bgcolor="#E6E6FA"><font size="2">80.7</font></td>
      <td bgcolor="#E6E6FA"><font size="2">6.6</font></td>
      <td bgcolor="#E6E6FA"><font size="2">406.9</font></td>
      <td bgcolor="#E6E6FA"><font size="2">91.8</font></td>
      <td bgcolor="#E6E6FA"><font size="2">1406</font></td>
      <td bgcolor="#E6E6FA"><font size="2">15.44</font></td>
    </tr>
    <tr align="right"> 
      <td bgcolor="#E6E6FA"><font size="2">18</font></td>
      <td bgcolor="#E6E6FA"><font size="2">74.6</font></td>
      <td bgcolor="#E6E6FA"><font size="2">6.3</font></td>
      <td bgcolor="#E6E6FA"><font size="2">332.3</font></td>
      <td bgcolor="#E6E6FA"><font size="2">78.8</font></td>
      <td bgcolor="#E6E6FA"><font size="2">1311</font></td>
      <td bgcolor="#E6E6FA"><font size="2">15.44</font></td>
    </tr>
    <tr align="right"> 
      <td bgcolor="#E6E6FA"><font size="2">19</font></td>
      <td bgcolor="#E6E6FA"><font size="2">56.4</font></td>
      <td bgcolor="#E6E6FA"><font size="2">3.7</font></td>
      <td bgcolor="#E6E6FA"><font size="2">275.8</font></td>
      <td bgcolor="#E6E6FA"><font size="2">56.1</font></td>
      <td bgcolor="#E6E6FA"><font size="2">1026</font></td>
      <td bgcolor="#E6E6FA"><font size="2">15.45</font></td>
    </tr>
    <tr align="right"> 
      <td bgcolor="#E6E6FA"><font size="2">20</font></td>
      <td bgcolor="#E6E6FA"><font size="2">59.4</font></td>
      <td bgcolor="#E6E6FA"><font size="2">4.6</font></td>
      <td bgcolor="#E6E6FA"><font size="2">216.4</font></td>
      <td bgcolor="#E6E6FA"><font size="2">45.8</font></td>
      <td bgcolor="#E6E6FA"><font size="2">1073</font></td>
      <td bgcolor="#E6E6FA"><font size="2">15.45</font></td>
    </tr>
    <tr align="right"> 
      <td bgcolor="#E6E6FA"><font size="2">21</font></td>
      <td bgcolor="#E6E6FA"><font size="2">33.9</font></td>
      <td bgcolor="#E6E6FA"><font size="2">2.1</font></td>
      <td bgcolor="#E6E6FA"><font size="2">182.5</font></td>
      <td bgcolor="#E6E6FA"><font size="2">33.7</font></td>
      <td bgcolor="#E6E6FA"><font size="2">673</font></td>
      <td bgcolor="#E6E6FA"><font size="2">15.48</font></td>
    </tr>
    <tr align="right"> 
      <td bgcolor="#E6E6FA"><font size="2">22</font></td>
      <td bgcolor="#E6E6FA"><font size="2">33.8</font></td>
      <td bgcolor="#E6E6FA"><font size="2">2.0</font></td>
      <td bgcolor="#E6E6FA"><font size="2">148.6</font></td>
      <td bgcolor="#E6E6FA"><font size="2">26.4</font></td>
      <td bgcolor="#E6E6FA"><font size="2">672</font></td>
      <td bgcolor="#E6E6FA"><font size="2">15.48</font></td>
    </tr>
    <tr align="right"> 
      <td bgcolor="#E6E6FA"><font size="2">Un</font></td>
      <td bgcolor="#E6E6FA"><font size="2">1.4</font></td>
      <td bgcolor="#E6E6FA"><font size="2">0.03</font></td>
      <td bgcolor="#E6E6FA"><font size="2">147.3</font></td>
      <td bgcolor="#E6E6FA"><font size="2">10.0</font></td>
      <td bgcolor="#E6E6FA"><font size="2">164</font></td>
      <td bgcolor="#E6E6FA"><font size="2">16.96</font></td>
    </tr>
    <tr align="right"> 
      <td bgcolor="#E6E6FA"><font size="2">X</font></td>
      <td bgcolor="#E6E6FA"><font size="2">147.3</font></td>
      <td bgcolor="#E6E6FA"><font size="2">14.6</font></td>
      <td bgcolor="#E6E6FA"><font size="2">&nbsp;</font></td>
      <td bgcolor="#E6E6FA"><font size="2">4.8</font></td>
      <td bgcolor="#E6E6FA"><font size="2">2327</font></td>
      <td bgcolor="#E6E6FA"><font size="2">15.57</font></td>
    </tr>
  </table>
</div>
<p>The Human Chromosomes can be obtained from the NCBI ftp site: <a href="ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/">ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/</a></p>
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