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<span class="navon">Plasmodium<br>
falciparum</span><span class="navoff"><br>
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</span><a href="third.html" class="navoff">Third Party<br>
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<p><br>
<br>
<br>
<span class="headlines"><em>Plasmodium falciparum</em> Arrives in GenBank</span></p>
<br>
<span class="bodycopy">The recently completed genome
of the malaria parasite <em>Plasmodium
falciparum</em> is available in GenBank and displayed in the Entrez Map Viewer.
As reported in the October 3rd, 2002 issue of Nature (search
in PubMed for PMID 12368864),
<em>P. falciparum</em> clone 3D7 consists
of a 23-megabase nuclear genome
of 14 chromosomes assembled
from finished high-throughput genomic sequence (HTGS, Phase 3). The genome
was sequenced by
members of the Malaria Genome Sequencing Consortium including The Institute
for Genomic Research (TIGR), in collaboration with the US Naval Medical
Research Center, the Sanger Institute, and the Stanford Genome Technology
Center at Stanford
University.<br>
<br>
</span><a href="javascript:;" onClick="MM_openBrWindow('entrez_lrg.html','Cn3D','scrollbars=yes,resizable=yes,width=500,height=400')"><img width="488" height="467" longdesc="Figure 1: Entrez Map Viewer display of BLAST hit to chromsome 9 of P. falciparum for unknown Arabidopsis protein BAB01718. The BLAST hit coincides with P. falciparum protein NP_704698, as seen on the Gene map, and predicted protein EAA19956 from P. yoelii, as seen on the &#8220;Py prot&#8221; map." src="images/entrez_sm.gif" border="1"></a><a href="#" onClick="MM_openBrWindow('model_lrg.html','Figure','scrollbars=yes,width=580,height=523')"></a> <br>
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<a href="#" onClick="MM_openBrWindow('model_lrg.html','Figure','scrollbars=yes,width=580,height=523')"><br>
</a><span class="captions">Figure 1:</span><span class="captions2">&nbsp;Entrez
Map Viewer display of BLAST hit to chromosome 9 of <em>P. falciparum</em> for unknown
<em>Arabidopsis</em> protein BAB01718. The BLAST hit coincides with <em>P. falciparum</em>
protein NP_704698, as seen on the Gene map, and predicted protein EAA19956
from <em>P. yoelii</em>, as seen on the &#8220;Py prot&#8221; map. </span><span class="bodycopy"><br>
<br>
</span> <span class="bodycopy"> The sequence of each
<em>P. falciparum</em> chromosome is represented in the Entrez Genomes database
as a separate RefSeq record (with accession number of
the form NC_XXXXXX ) and may be found by the query &#8220;<em>Plasmodium
falciparum</em> 3D7[organism]&#8221; in the Entrez Genomes. <br>
<br>
The Entrez document summary
for the sequence of chromosome
9, returned by the above query,
appears as follows:
<br>
<br>
</span>
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<td width="88" class="tables">&nbsp;</td>
<td width="400" class="tables"><span class="tables">NC_004330 <br>
Plasmodium falciparum 3D7 <br>
chromosome 9,<br>
complete sequence[99]<br>
gi|23613523|ref|NC_004330.1|</span> </td>
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</table>
</td>
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<span class="bodycopy"> <br>
</span><span class="bodycopy">
</span>
<span class="authors">
</span><span class="bodycopy">The accession number in the document summary is a link to a Map
Viewer display of the assembled sequence data, gene annotations,
and genetic linkages.<br>
<br>
Sequence maps available in the
Map Viewer for <em>P. falciparum</em> include Chromosome, Component,
and Gene maps. The chromosome sequence map shows the genomic sequence
assembled from smaller
components,
visible on the components map. The genes sequence
map displays genes that have been annotated on the chromosome including
known and putative genes placed using blastx alignments of
reference sequence proteins to
the chromosome sequence. Another informative map is the &#8220;Py Protein&#8221; map,
which presents reciprocal
best hits between predicted proteins encoded in the <em>P. falciparum</em> genome
and those predicted to
be encoded in the whole genome shotgun (WGS) sequences of
<em>P. yoelii</em>, a rodent malaria parasite. The order of the hits
shown on the &#8220;Py
protein&#8221; map reflects the order of the corresponding genes on the <em>P. falciparum</em> &#8220;gene_seq&#8221; map.<br>
<br>
A Genome BLAST against the <em>P. falciparum</em> genome using unidentified <em>A.
thaliana</em> protein BAB01718 leads to the genome view shown in the
figure above. Note the hit to the <em>P. falciparum</em> genome in an
area encoding a protein that is a reciprocal best hit to a <em>P. yoelii</em> protein.<br>
<br>
A variety of <em>Plasmodium</em> data has been incorporated into a malaria-related
resource called Malaria
Triad: Genetics &amp; Genomics that
is available from NCBI at:</span><span class="authors"><br>
</span><span class="bodycopy"><br>
</span>
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<td><table width="488" height="20" border="0" cellpadding="8" cellspacing="0">
<tr>
<td width="88" class="tables">&nbsp;</td>
<td width="400" class="tables"><a href="http://www.ncbi.nlm.nih.gov/projects/Malaria/">www.ncbi.nlm.nih.gov/projects/Malaria/</a></td>
</tr>
</table>
</td>
</tr>
</table>
<span class="bodycopy"> <br>
</span><span class="authors">
</span>
<span class="bodycopy">
The site combines information on the organisms involved in malaria research
and provides access to
services for data retrieval, genetic and genomic analysis of the sequence
data, and malaria-related news. The Plasmodium genomes data (<em>P. falciparum,
P. yoelii</em> and
<em>P. vivax</em>), as well the genome of <em>Anopheles gambiae</em>, can be accessed from
the malaria page along with
the results of pre-computed sequence and literature searches. BLAST services
have been tailored
to search against malaria-related organisms and the <em>Plasmodium
falciparum</em> and <em>Plasmodium yoelii</em> genomes have been incorporated into
Genome BLAST (see figure 1),
in which BLAST results are displayed in their genomic context using the
Entrez Map Viewer.<br>
<br>
The <em>P. falciparum</em> genome can
be downloaded from the NCBI
FTP site at:
<table width="488" height="20" border="0" cellpadding="1" cellspacing="0" bgcolor="#CCDFFF">
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<td><table width="488" height="20" border="0" cellpadding="8" cellspacing="0">
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<td width="88" class="tables">&nbsp;</td>
<td width="400" class="tables"><a href="ftp://ftp.ncbi.nih.gov/genbank/genomes/P_falciparum">ftp.ncbi.nih.gov/genbank/genomes/P_falciparum/</a></td>
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<span class="bodycopy"> </span><span class="bodycopy"><br>
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