1 line
No EOL
9.7 KiB
HTML
1 line
No EOL
9.7 KiB
HTML
<html lang="eng">
|
|
|
|
|
|
<head>
|
|
<meta http-equiv="content-type" content="text/html;charset=iso-8859-1">
|
|
<meta name="generator">
|
|
<title>NCBI News | Fall 2001</title>
|
|
<style type="text/css">
|
|
<!--
|
|
a:hover { color: 993300; text-decoration:underline}
|
|
-->
|
|
</style>
|
|
</head>
|
|
|
|
|
|
<body background="images/bckgrnd.gif" bgcolor="white" link="#003399" alink="#003399" vlink="#003399" text="black">
|
|
<span class="heads"></span> <span class="subheads"></span>
|
|
<table border="0" cellpadding="0" cellspacing="0" valign="left">
|
|
<tr height="176">
|
|
|
|
<td height="176" colspan="2" valign="left" align="left"><img height="12" width="8" src="images/dotclear.gif" alt=" "><img height="171" width="173" src="images/logo.gif" alt="NCBI Logo"></td>
|
|
|
|
<td height="176" valign="top" width="10" align="left"></td>
|
|
|
|
<td height="176" valign="top" width="420"><img height="80" width="364" src="images/msthd1.gif" border="0" alt="NCBI News" usemap="#E">
|
|
<map name="E">
|
|
<area href="http://www.ncbi.nlm.nih.gov/About/newsletter.html" coords="1,16,362,71" shape="rect" alt="NCBI News Masthead" title="NCBI News Masthead">
|
|
</map><br>
|
|
<table width="420" border="0" cellspacing="0" cellpadding="0">
|
|
<tr valign="top">
|
|
<td height="80"><img height="80" width="340" src="images/msthd1a.gif" border="0" alt="National Center for Biotechnology Information" usemap="#NCBI">
|
|
<map name="NCBI">
|
|
<area href="http://www.nih.gov" coords="0,60,139,77" shape="rect" alt="National Institutes of Health" title="National Institutes of Health">
|
|
<area href="http://www.nlm.nih.gov" coords="0,41,138,53" shape="rect" alt="National Library of Medicine" title="National Library of Medicine">
|
|
<area href="http://www.ncbi.nlm.nih.gov" coords="0,14,253,29" shape="rect" alt="Nation Center for Biotechnology Information" title="Nation Center for Biotechnology Information">
|
|
</map>
|
|
</td>
|
|
<td height="80"><img height="80" width="80" src="images/edition.gif" alt="Fall 2001"></td>
|
|
</tr>
|
|
</table>
|
|
</td>
|
|
</tr>
|
|
<tr valign="top">
|
|
|
|
<td width="13" align="left" valign="top"><img height="10" width="13" src="images/dotclear.gif" alt=" "></td>
|
|
|
|
<td width="173" align="left" valign="top">
|
|
<p><font size="2" face="Arial,Helvetica,sans-serif"><br>
|
|
<br>
|
|
<img height="33" width="178" src="images/issue.gif" alt="In this issue..."><br>
|
|
<b><br>
|
|
Using TaxPlot to<br>
|
|
Compare Genomes<br>
|
|
<br>
|
|
</b> <font color="#003399"><a href="refseq.html"><b>New RefSeq Accession<br>
|
|
Numbers for Curated<br>
|
|
Genomic Regions<br>
|
|
</b></a> <b><br>
|
|
<a href="genbank.html">GenBank News<br>
|
|
</a> <br>
|
|
<a href="recentpubs.html">Recent Publications<br>
|
|
</a> <br>
|
|
<a href="dart.html">DART Targets<br>
|
|
Protein Domains<br>
|
|
</a> <br>
|
|
<a href="evidence.html">Evidence Viewer<br>
|
|
Facilitates Analysis<br>
|
|
of NCBI Human<br>
|
|
Gene Models<br>
|
|
</a> <br>
|
|
<a href="faqs.html">Frequently Asked<br>
|
|
Questions<br>
|
|
</a> <br>
|
|
<a href="blastlab.html">BLAST Lab<br>
|
|
</a> <br>
|
|
<a href="masthead.html">Masthead</a><br>
|
|
<br>
|
|
<br>
|
|
</b></font><font face="Times New Roman, Times, serif" size="3"> </font></font></p>
|
|
<table width="150" border="0" cellspacing="0" cellpadding="1" bgcolor="#FFFFFF">
|
|
<tr bgcolor="003399">
|
|
<td width="150">
|
|
<table border="0" cellspacing="0" cellpadding="11" bgcolor="#FFFFFF" width="150">
|
|
<tr bordercolor="003399">
|
|
<td bordercolor="003399" width="150"><font face="Arial,Helvetica,sans-serif" size="2"><font face="Times New Roman, Times, serif" size="3"><font face="Arial, Helvetica, sans-serif" size="2" color="003399"><b>Notice
|
|
to Subscribers<br>
|
|
<br>
|
|
</b> For your records, there was no Summer 2001 issue of <i>NCBI
|
|
News.</i></font></font></font></td>
|
|
</tr>
|
|
</table>
|
|
</td>
|
|
</tr>
|
|
</table>
|
|
<p><font size="2" face="Arial,Helvetica,sans-serif"><font color="#003399"><b>
|
|
</b></font></font></p>
|
|
</td>
|
|
|
|
<td width="10" valign="left" bordercolor="003399"> </td>
|
|
<td width="420" bordercolor="003399">
|
|
<div valign="left">
|
|
<p><br>
|
|
<br>
|
|
<font face="Arial, Helvetica, sans-serif" size="3" color="003399"><b>Using
|
|
TaxPlot to Compare Genomes</b></font></p>
|
|
<p><font face="Times New Roman, Times, serif" size="3" color="#000000"><br>
|
|
TaxPlot is a tool for 3-way comparisons of genomes on the basis of the
|
|
protein sequences they encode. To use TaxPlot, one selects a reference
|
|
genome to which two other genomes are compared. Pre-computed BLAST results
|
|
are then used to plot a point for each predicted protein in the reference
|
|
genome, based on the best alignment with proteins in each of the two
|
|
genomes being compared. <br>
|
|
<br>
|
|
Figure 1 shows a TaxPlot in which <i>E. coli</i> K12 has been selected
|
|
as the reference genome for comparison of two strains of <i>H. pylori</i>,
|
|
J99 and 26695. Each point in the figure represents a single <i>E. coli</i>
|
|
protein. The X and Y coordinates represent the BLAST score for the protein’s
|
|
closest match in the two strains of <i>H. pylori</i>. There are 217
|
|
<i>E. coli</i> proteins that are equally similar to proteins in the
|
|
two <i>H. pylori</i> strains, as shown by the points lying on the central
|
|
diagonal. <i>E. coli</i> has 678 proteins with greater similarity to
|
|
<i> H. pylori</i> strain J99 (if only marginally), and 687 proteins
|
|
with greater similarity to <i>H. pylori</i> strain 26695.<br>
|
|
<br>
|
|
<img src="images/figure1.gif" width="420" height="349" border="1" alt="Chart showing Distribution of E. Coli K12 homologs"><br>
|
|
<br>
|
|
<b><font face="Arial,Helvetica,sans-serif" size="2" color="#003399">Figure
|
|
1:</font></b> <font color="003399" size="2">TaxPlot for two strains
|
|
of <i>H. pylori</i> against E. coli as the reference genome. Points
|
|
representing proteins involved in amino acid transport and metabolism
|
|
are highlighted in blue.</font><font color="003399"><br>
|
|
</font> <br>
|
|
Overall, the proteomes of the two <i>H. pylori</i> strains appear to
|
|
be equally similar to that of <i>E. coli</i>. However, a few significant
|
|
differences between the <i>H. pylori</i> strains show up as off-diagonal
|
|
points toward the left-hand portion of the plot. These points represent
|
|
proteins in E. coli that better match in one strain of <i>H. pylori</i>
|
|
than in the other.<br>
|
|
<br>
|
|
For instance, a number of <i>E. coli</i> proteins have low BLAST scores
|
|
against the <i>H. pylori</i> J99 strain, yet relatively high BLAST scores
|
|
against the 26695 strain. These points may represent cases in which
|
|
selection pressures operating on the orthologs of these <i>E. coli</i>
|
|
proteins in the two <i>H. pylori</i> strains are different. To determine
|
|
if there is a pattern to these differences, one may identify individual
|
|
points on the plot to learn the function of the <i>E. coli</i> proteins
|
|
indicated.<br>
|
|
<br>
|
|
Subsets of the points plotted can be selected by simply clicking on
|
|
an area of the graph or by using a menu box to select proteins by functional
|
|
class. Hyperlinks to the BLAST2 Sequences service provide displays of
|
|
pairwise alignments. In the figure, those proteins known in <i>E. coli</i>
|
|
to be involved in amino-acid transport and metabolism have been selected
|
|
and appear blue in the plot. Note that most of the off-diagonal proteins
|
|
of this type are more similar to proteins from H. pylori strain 26695
|
|
than J99, suggesting that <i>H. pylori</i> strain J99 may be undergoing
|
|
a restructuring of some aspects of its amino acid processing systems.
|
|
Such restructuring could represent an important adaptation in the J99
|
|
strain of relevance to its pathogenesis.<br>
|
|
<br>
|
|
The TaxPlot tool is accessible from the <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Genome">Entrez
|
|
Genomes</a> Web page, under Tools and Analysis. In addition to the microbial
|
|
genome version described here, there is also a TaxPlot service for eukaryotic
|
|
genomes.<br>
|
|
<br>
|
|
<br>
|
|
</font><font face="Times New Roman, Times, serif" size="3" color="#000000">
|
|
</font> </p>
|
|
<p align="right"><a href="refseq.html"><img height="27" width="69" src="images/continue.gif" border="0" alt="Continue"></a><br>
|
|
<div align="right"><font color="#003399"> </font></div>
|
|
<font color="#003399">
|
|
<hr noshade size="1" align="right" width="420">
|
|
</font>
|
|
<div align="right"><img height="32" width="158" src="images/foot.gif" border="0" alt="NCBI News | Spring 2000" usemap="#NCBI News foot">
|
|
<map name="NCBI News foot">
|
|
<area href="http://www.ncbi.nlm.nih.gov/About/newsletter.html" coords="0,9,196,34" shape="rect" alt="NCBI News Footer" title="NCBI News Footer">
|
|
</map>
|
|
<br>
|
|
<br>
|
|
<br>
|
|
</div>
|
|
<p class="body_text"> </p>
|
|
</div>
|
|
</td>
|
|
</tr>
|
|
</table>
|
|
</body>
|
|
|
|
</html> |