182 lines
No EOL
16 KiB
HTML
182 lines
No EOL
16 KiB
HTML
<html lang="eng">
|
|
|
|
|
|
<head>
|
|
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
|
|
<meta name="generator">
|
|
<title>NCBI News:Volume 15, Issue 1|New Databases and Tools Target Influenza</title>
|
|
<link rel="stylesheet" href="ncbinews.css" type="text/css">
|
|
<link rel="stylesheet" href="ncbinews.css" type="text/css">
|
|
<script language="JavaScript" type="text/JavaScript">
|
|
<!--
|
|
function MM_goToURL() { //v3.0
|
|
var i, args=MM_goToURL.arguments; document.MM_returnValue = false;
|
|
for (i=0; i<(args.length-1); i+=2) eval(args[i]+".location='"+args[i+1]+"'");
|
|
}
|
|
|
|
function MM_openBrWindow(theURL,winName,features) { //v2.0
|
|
window.open(theURL,winName,features);
|
|
}
|
|
//-->
|
|
</script>
|
|
<style type="text/css">
|
|
<!--
|
|
a:hover { color: 993300; text-decoration:underline}
|
|
.style2 {font-family: "Courier New", Courier, monospace; font-size: x-small; color: #000000; }
|
|
.style4 {color: #003399}
|
|
.style5 {font-size: 10px}
|
|
.style6 {font-size: 12px}
|
|
-->
|
|
</style>
|
|
</head>
|
|
|
|
|
|
<body background="images/bckgrnd.gif" bgcolor="white" link="#003399" alink="#CC6600" vlink="#003399" text="black" leftmargin="5" topmargin="5" marginwidth="5" marginheight="5"><span class="heads"></span> <span class="subheads"></span>
|
|
<table border="0" cellpadding="0" cellspacing="0" valign="left" class="tables">
|
|
<!--DWLayoutTable-->
|
|
<tr height="176">
|
|
<td height="176" colspan="2" valign="left" align="left"><img height="12" width="8" src="images/dotclear.gif" alt=""><a href="http://www.ncbi.nlm.nih.gov"><img src="images/logo.gif" alt="NCBI Logo" width="173" height="171" border="0"></a></td>
|
|
<td valign="top" width="10" align="left"></td>
|
|
<td colspan="2" valign="top"><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="1,17,362,72" shape="rect" alt="NCBI News banner" title="NCBI News Masthead">
|
|
</map>
|
|
<br>
|
|
<table width="488" border="0" cellspacing="0" cellpadding="0">
|
|
<tr valign="top">
|
|
<td width="380" height="86"><img height="80" width="340" src="images/msthd1b.gif" border="0" alt="National Center for Biotechnology Information" usemap="#NCBI" vspace="3">
|
|
<map name="NCBI">
|
|
<area href="http://www.dhhs.gov" coords="0,60,221,74" shape="rect" alt="US Department of Health and Human Services" title="US Department of Health and Human Services">
|
|
<area href="http://www.ncbi.nlm.nih.gov" coords="0,6,268,21" shape="rect" alt="National Center for Biotechnology Information" title="National Center for Biotechnology Information">
|
|
<area href="http://www.nlm.nih.gov" coords="0,24,147,36" shape="rect" alt="National Library of Medicine" title="National Library of Medicine">
|
|
<area href="http://www.nih.gov" coords="0,42,147,56" shape="rect" alt="National Institutes of Health" title="National Institutes of Health">
|
|
</map> </td>
|
|
<td width="108" height="86">
|
|
<div align="right"><img name="edition1" src="images/edition1.gif" width="125" height="79" border="0" alt="Vol 14 No 1 of NCBI News"></div> </td>
|
|
</tr>
|
|
</table> </td>
|
|
</tr>
|
|
<tr valign="top">
|
|
<td width="13" rowspan="2" align="left" valign="top"><img height="10" width="13" src="images/dotclear.gif" alt=" "></td>
|
|
<td width="173" height="1578" align="left" valign="top">
|
|
<table border="0" cellpadding="0" cellspacing="0" width="120" valign="left" name="Navigation">
|
|
<tr height="36">
|
|
<td width="130" height="36" valign="top"><br>
|
|
<a href="http://www.ncbi.nlm.nih.gov/About/newsletter.html"><img src="images/pastissue.gif" alt="click to go to index of past issues" width="120" height="33" border="0"></a><br>
|
|
<br>
|
|
|
|
<img height="33" width="120" alt="In this issue" src="images/issue.gif"><br>
|
|
<br>
|
|
<span class="links2"><br>
|
|
</span>
|
|
<span class="navon">Influenza Database and Tools </span><br>
|
|
<br>
|
|
<a href="trace.html" class="navoff">Trace Archives at 1 Billion </a><br>
|
|
<br>
|
|
<a href="nucsplit.html" class="navoff">Entrez Nucleotide Split Database </a><br>
|
|
<br>
|
|
<a href="tpa.html" class="navoff">Third Party Annotation Database </a><br>
|
|
<br>
|
|
<a href="refseq.html" class="navoff">RefSeq Release 18 </a><br>
|
|
<br>
|
|
<a href="1918.html" class="navoff">1918 Killer Flu Virus</a><br>
|
|
<br>
|
|
<a href="unigene.html" class="navoff">UniGene</a><br>
|
|
<br>
|
|
<a href="GBrel.html" class="navoff">GenBank Release 155</a><br>
|
|
<br>
|
|
<a href="mammoth.html" class="navoff">Mammoths and Moas at NCBI</a><br>
|
|
<br>
|
|
<a href="pubs.html" class="navoff">Recent NCBI Publications</a><br>
|
|
<br>
|
|
<a href="papers.html" class="navoff">NCBI Papers Most Cited</a><br>
|
|
<br>
|
|
<a href="courses.html" class="navoff">NCBI Courses</a><br>
|
|
<br>
|
|
<a href="blastlab.html" class="navoff">BLAST Lab</a><br>
|
|
<br>
|
|
<a href="ngenb.html" class="navoff">Genome Builds and Map Viewer</a><br>
|
|
<br>
|
|
<br><a href="masthead.html" class="navoff">Masthead</a> </td>
|
|
</tr>
|
|
</table> <p> </p></td>
|
|
<td valign="left" bordercolor="003399"></td>
|
|
<td width="492" rowspan="2" valign="top">
|
|
<div valign="left">
|
|
<p><br>
|
|
<br>
|
|
<span class="headlines"><a name="1"></a>New Databases and Tools Target Influenza</span></p>
|
|
<p class="bodycopy">Influenza virus infection is a major threat to public health in the United States, resulting in over 200,000 hospitalizations and 30,000 deaths each year. The Influenza Virus Genome Project [<span class="footnote style6"><a href="#fn1">1</a></span>] is providing researchers with a growing collection of virus sequences essential to the identification of the genetic determinants of influenza pathogenicity. NCBI provides online tools for the analysis of these and other influenza sequences in GenBank that allow researchers to:</p>
|
|
<p class="bodycopy"> <strong>Retrieve—</strong>viral genomic, gene encoding, or protein sequences and download them in a number of formats</p>
|
|
<p class="bodycopy"><strong>Align—</strong>locally stored sequences with those in NCBI databases </p>
|
|
<p class="bodycopy"><strong>Cluster—</strong>sequences for phylogenetic analysis using a variety of algorithms and weight matrices, constructing dendrograms from the result </p>
|
|
<p class="bodycopy"><strong>Download—</strong>complete genomic sequences </p>
|
|
<p class="bodycopy"><strong>Search—</strong>influenza sequences using BLAST® </p>
|
|
<p class="bodytext3">An Example</p>
|
|
<p class="bodycopy">The analysis of the coding region (CDS) of the hemagglutinin ('HA'), sequence for influenza virus A, GenBank® accession <strong>AY653200</strong>, serves as an example of the use of these tools to classify a new sequence. Prior to the analysis, the CDS portion of the sequence was downloaded in FASTA format using NCBI's Entrez, and the FASTA definition line was changed from:</p>
|
|
<p class="style2">>gi-50365728:29-1735 Influenza A virus(/chicken/Jilin/9/2004(H5N1))segment 4, complete sequence</p>
|
|
<p class="bodycopy">to read:</p>
|
|
<p class="style2">>local chicken</p>
|
|
<p class="bodytext3">Selection of influenza sequences for analysis</p>
|
|
<p class="bodycopy">To begin, use the Database link from the Influenza Virus Resource page at</p>
|
|
<table width="488" border="0" cellspacing="1" cellpadding="0">
|
|
<tr>
|
|
<td width="488" height="25" align="center" bgcolor="#dfefff"><div align="center" class="links2">
|
|
<p class="links2"><a href="http://www.ncbi.nlm.nih.gov/genomes/FLU/FLU.html">www.ncbi.nlm.nih.gov/genomes/FLU/FLU.html</a></p>
|
|
</div> </td>
|
|
</tr>
|
|
</table>
|
|
<span class="bodycopy"><br>
|
|
to reach the Query Builder shown in Fig. 1.
|
|
</p>
|
|
</span>
|
|
<p align="center"><img src="images/inf1sm.gif" alt="click for larger image" width="460" height="265" border="1" onClick="MM_openBrWindow('inf1large.htm','largerimage','scrollbars=yes,resizable=yes,width=980,height=565')"></p>
|
|
<p><font color="#000000">Click on image to view larger</font></p>
|
|
<p align="left"><b><span class="captions">Figure 1</span></b><span class="captions">.</span> <span class="captions2">Query Builder for influenza sequences. Queries are built by making selections in three different sections of the form, labeled A, B, and C</span></p>
|
|
<p class="bodycopy">Check the 'Coding region' radio button, indicated in section A, to specify the type of sequence to retrieve.</p>
|
|
<p class="bodycopy">From the menus in section B, select 'Influenza A', 'Avian', 'Asia', and 'HA' as the 'Virus Species', 'Host', Country/Region', and 'Segment', respectively. In addition, check 'Full-length sequences only' and restrict the search to H5N1 subtype sequences from the year 2005 using the check boxes and text fields in section C. Clicking on 'Add to Query Builder' will return the number of sequences that match, as shown in section D. Click on 'Get sequences' to generate the form shown in Fig. 2, containing a table of summaries for the 85 selected sequences. </p>
|
|
<p align="center" class="bodycopy"><img src="images/inf2sm.gif" alt="Influenza Figure 2" width="460" height="109" border="1" onClick="MM_openBrWindow('inf2large.htm','largerimage','scrollbars=yes,resizable=yes,width=952,height=225')"></p>
|
|
<p><font color="#000000">Click on image to view larger</font></p>
|
|
<p align="left"><b><span class="captions">Figure 2. </span></b><span class="captions"></span> <span class="captions2">Selection of sequences for further analysis. For brevity, only the first three of 85 selected entries is shown. </span></p>
|
|
<p class="bodycopy">The table is sortable and the controls in section A have been used to sort the records by "Virus Name", after which 10 sequences from various hosts (3 goose, 1 quail, 2 duck, 2 chicken, 1 gull, 1 heron) have been selected for further analysis using the check boxes next to each entry-only the first two of the checked entries are visible in the figure. Using the button in section B, the FASTA sequence called "local chicken" has been uploaded, as indicated in section C. </p>
|
|
<p class="bodytext3"><a name="2"></a>Multiple sequence alignment</p>
|
|
<p class="bodycopy">Click on 'Do multiple alignment' to align the "local chicken" sequence to the selected 85 database sequences using the multiple sequence alignment program MUSCLE [<span class="footnote style6"><a href="#fn2">2</a></span>], to generate the alignment shown in Fig. 3. </p>
|
|
<p align="center" class="bodycopy"><img src="images/inf3sm.gif" alt="Influenza Figure 3" width="460" height="132" border="1" onClick="MM_openBrWindow('inf3large.htm','largerimage','scrollbars=yes,resizable=yes,width=992,height=284')"></p>
|
|
<p><font color="#000000">Click on image to view larger</font></p>
|
|
<p align="left"><b><span class="captions">Figure 3.</span></b><span class="captions"></span> Multiple sequence alignment for the "local chicken" HA sequences and 10 influenza HA coding sequences selected from the NCBI databases<span class="captions2">.</span></p>
|
|
<p class="bodycopy">The portion of the alignment displayed, indicated in section A, begins near base 950 and ends near base 1040. Two major groups of sequences, characterized by non-synonymous base changes, sections B, one synonymous base change, section C, and a three-base deletion, section D, are evident. </p>
|
|
<p class="bodytext3">Clustering and Phylogenetic analysis</p>
|
|
<p class="bodycopy">Click on 'Build a Tree' to invoke the setup page for phylogenetic analysis where the sequences may be selected for inclusion in the subsequent analysis using check boxes. Click on 'Phylogenetic Analysis' to display the next page where a clustering algorithm may be selected, and the tree built. The resulting dendrogram is shown in Fig. 4.</p>
|
|
<p align="center" class="bodycopy"><img src="images/inf4sm.gif" alt="Influenza Figure 4" width="460" height="145" border="1" onClick="MM_openBrWindow('inf4large.htm','largerimage','scrollbars=yes,resizable=yes,width=636,height=201')"></p>
|
|
<p><font color="#000000">Click on image to view larger</font></p>
|
|
<p align="left"><b><span class="captions">Figure 4 </span></b>.Dendrogram built using the Local Search Neighbor Joining method. <span class="captions2"></span> </p>
|
|
<p class="bodycopy"><a name="3"></a>The dendrogram shows two clusters, as might be anticipated on the basis of the alignment of Fig. 3. Two influenza sequences from a goose host and one from a gull host lie in the first of these clusters while three from a chicken host, including our "local chicken" sequence, two from a duck and one from a heron host are in the second cluster. An outlying sequence, branching from the base of the tree, came from a goose host in Mongolia. The dendrogram may be recomputed after adjusting several parameters. A 'non-linear' two dimensional dot plot (not shown) that groups sequences to provide an overview of a large dataset may also be generated.</p>
|
|
<p class="bodycopy">Phylogenetic comparisons of this type have provided valuable insight into the process of genomic reassortments in influenza that lead to influenza outbreaks [<span class="footnote style6"><a href="#fn3">3</a></span>]. </p>
|
|
<p align="right" class="bodycopy"><span class="authors style4">—TT</span></p>
|
|
<p align="left" class="bodycopy"><a name="fn1"></a>[<span class="footnote style5 style6">1</span>]Ghedin E, et al. Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution. <em>Nature</em>. 2005 Oct 20;437(7062):1162-6. Epub 2005 Oct 5. <span class="style4">PMID: <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=PureSearch&db=pubmed&details_term=16208317[UID]">16208317</a></span>.<a href="#1"><img src="images/arrowupblue.gif" alt="back to article" width="10" height="15" border="0"></a></p>
|
|
<p class="bodycopy"><a name="fn2"></a>[<span class="footnote style6">2</span>]Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. <em>Nucleic Acids Res</em>. 2004 Mar 19;32(5):1792-7. Print 2004. <span class="style4">PMID: <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=PureSearch&db=pubmed&details_term=15034147[UID]">15034147</a></span> <a href="#2"><img src="images/arrowupblue.gif" alt="back to article" width="10" height="15" border="0"></a></p>
|
|
<p class="bodycopy"><a name="fn3"></a>[<span class="footnote style6">3</span>]Holmes EC, et al. Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses. <em>PLoS Biol.</em> 2005 Sep;3(9):e300. Epub 2005 Jul 26. <span class="style4">PMID: <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=PureSearch&db=pubmed&details_term=1602618[UID]">1602618</a></span> <a href="#3"><img src="images/arrowupblue.gif" alt="back to article" width="10" height="15" border="0"></a></p>
|
|
<p align="right" class="bodycopy"><a href="trace.html"><img height="27" width="69" src="images/continue.gif" border="0" alt="to next article" title="to Probe Database"></a></p>
|
|
<hr noshade size="1" align="right" width="488">
|
|
<p align="right" class="bodycopy"><img name="foot1" src="images/foot1.gif" width="187" height="32" border="0" usemap="#m_foot1" alt="NCBI News | Summer 2003"><map name="m_foot1">
|
|
<area shape="rect" coords="0,8,185,30" href="http://www.ncbi.nlm.nih.gov/About/newsletter.html" title="NCBI News" alt="NCBI News" >
|
|
</map>
|
|
<br>
|
|
</p>
|
|
</div></td>
|
|
<td width="15"> </td>
|
|
</tr>
|
|
<tr valign="top">
|
|
<td height="1578"> </td>
|
|
<td valign="left" bordercolor="003399"></td>
|
|
<td> </td>
|
|
</tr>
|
|
</table>
|
|
<p class="bodytext4"> </p>
|
|
<p class="captions2"> </p>
|
|
<p class="tables2"> </p>
|
|
<p class="tables2"> </p>
|
|
<p class="tables2"> </p>
|
|
</body>
|
|
|
|
</html> |