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<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana">Dear Colleagues,<?xml:namespace
prefix = o ns = "urn:schemas-microsoft-com:office:office"
/><o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana"> <o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana">The Consortium for Maize Genomics
is pleased to announce the release of data and analysis from the second assembly
of ~200,000 methylation-filtered (MF) and High Cot (HC) genomic sequences
(Release 2.0) at <A
href="http://www.tigr.org/tdb/tgi/maize/">http://www.tigr.org/tdb/tgi/maize/</A>.
<o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana"><o:p> </o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana">Release 2.0 comprises four
assemblies: (1) MF-only (Release2.0MF), (2) HC-only (Release2.0HC), (3) MF and
HC combined (Release2.0ALL), (4) "Unfiltered" (UF) -only (random shotgun reads
generated from an unfiltered maize genomic library)
(Release2.0UF).<o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana"><o:p> </o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana">For <B>Release 2.0 assembly
statistics summary,</B> please visit: <A
href="http://www.tigr.org/tdb/tgi/maize/release2.0/assembly_summary.shtml">http://www.tigr.org/tdb/tgi/maize/release2.0/assembly_summary.shtml</A></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana"><o:p> </o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana">For <B>Sequencing progress to
date</B>, please visit:<o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana"><A
href="http://www.tigr.org/tdb/tgi/maize/progress_graph.shtml">http://www.tigr.org/tdb/tgi/maize/progress_graph.shtml</A><o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana"><o:p> </o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana">For <B>Analysis of repetitive
sequences in the maize genomic assemblies,</B> please visit: <A
href="http://www.tigr.org/tdb/tgi/maize/release2.0/repeat_analysis.shtml">http://www.tigr.org/tdb/tgi/maize/release2.0/repeat_analysis.shtml</A><o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana"><o:p> </o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana">For <B>Gene matches to maize
genomic sequences</B>, please visit:<o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana"><A
href="http://www.tigr.org/tdb/tgi/maize/release2.0/gene_matches.shtml">http://www.tigr.org/tdb/tgi/maize/release2.0/gene_matches.shtml</A><o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana"><o:p> </o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana">For <B>Mapping maize assemblies to
maize sequence markers</B>, please visit:<o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana"><A
href="http://www.tigr.org/tigr-scripts/tgi/marker2.annotator.pl?species=combo_marker">http://www.tigr.org/tigr-scripts/tgi/marker2.annotator.pl?species=combo_marker</A><o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana"><o:p> </o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana">In addition to the Release 2.0
data and BLAST server, we have<SPAN class=400340818-14082003> added
</SPAN>several new features <SPAN class=400340818-14082003>to </SPAN>our
website:<o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana"><o:p> </o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><B><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana">---GENOME MAP
BROWSER---<o:p></o:p></SPAN></B></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana">We have extended the 'Mapping
maize assemblies to maize sequence markers' page to include a genome map browser
which allows the user to take a closer look at specific chromosomal regions or
'bins'.<SPAN style="mso-spacerun: yes"> </SPAN>The genome map browser
provides links between maize sequence markers, maize tentative consensus (TC)
sequences from the TIGR Maize Gene Index (<A
href="http://www.tigr.org/tdb/tgi/zmgi/">http://www.tigr.org/tdb/tgi/zmgi/</A>),
maize genomic assemblies (AZMs for <U>A</U>ssembled <I><U>Z</U>ea
<U>m</U>ays</I>) and maize BAC contigs.<SPAN style="mso-spacerun: yes">
</SPAN>The genome map browser is located at: <A
href="http://www.tigr.org/tigr-scripts/tgi/print_chromosomes.pl">http://www.tigr.org/tigr-scripts/tgi/print_chromosomes.pl</A><o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana">and was built using tools provided
by the Generic Model Organism Database Project
(http://www.gmod.org/).<o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana"><o:p> </o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><B><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana">---BAC
VIEWER---<o:p></o:p></SPAN></B></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana">We took all maize genomic
sequences >10 kb from GenBank and searched against our maize AZMs using
BLAT.<SPAN style="mso-spacerun: yes"> </SPAN>In the BAC viewer the user
can select specific genomic sequences by accession number and view the
alignments of maize AZMs, annotated repetitive regions and maize, rice and
sorghum TC sequences.<SPAN style="mso-spacerun: yes"> </SPAN>The BAC
viewer is located at <A
href="http://www.tigr.org/tigr-scripts/tgi/BAC.annotator.pl">http://www.tigr.org/tigr-scripts/tgi/BAC.annotator.pl</A>
and was built using tools provided by the Generic Model Organism Database
Project (http://www.gmod.org/).<o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana"><o:p> </o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><B><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana">---BAC
ANNOTATION---<o:p></o:p></SPAN></B></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana">We took all maize genomic
sequences > 10 kb from GenBank and processed them using the Eukaryotic Genome
Control automated annotation pipeline at TIGR.<SPAN
style="mso-spacerun: yes"> </SPAN>The annotation results are available at:
<A
href="http://www.tigr.org/tigr-scripts/tgi/mz_egc_bac_annot.pl?project=maize&data=BAC">http://www.tigr.org/tigr-scripts/tgi/mz_egc_bac_annot.pl?project=maize&data=BAC</A>.<SPAN
style="mso-spacerun: yes"> </SPAN>We provide links to the predicted genes,
and include evidence supporting the gene structure predictions as well as an
annotation report for each individual sequence.<o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana"><o:p> </o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><B><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana">---MAIZE REPEAT
DATABASE---<o:p></o:p></SPAN></B></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana">We have compiled a database of
maize repetitive sequences<SPAN class=400340818-14082003> which
is</SPAN> available for download.<SPAN style="mso-spacerun: yes">
</SPAN>Please visit the following link for more information:</SPAN><FONT
face="Times New Roman" size=3> </FONT><U><SPAN
style="FONT-SIZE: 10pt; COLOR: blue; FONT-FAMILY: Verdana">http://www.tigr.org/tdb/tgi/maize/repeat_db.shtml
<o:p></o:p></SPAN></U></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana"><o:p> </o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><B><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana">---GENE ONTOLOGY
ASSIGNMENTS---<o:p></o:p></SPAN></B></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana">We have made automated Gene
Ontology assignments to the AZMs from the MF and HC combined assembly, based
on<SPAN class=400340818-14082003> significant</SPAN> hits to proteins with
an existing GO assignment.<o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><U><SPAN
style="FONT-SIZE: 10pt; COLOR: blue; FONT-FAMILY: Verdana">http://www.tigr.org/tdb/tgi/maize/release2.0/GO/GO.html<o:p></o:p></SPAN></U></P>
<DIV
style="BORDER-RIGHT: medium none; PADDING-RIGHT: 0in; BORDER-TOP: medium none; PADDING-LEFT: 0in; PADDING-BOTTOM: 1pt; BORDER-LEFT: medium none; PADDING-TOP: 0in; BORDER-BOTTOM: windowtext 2.25pt double">
<P class=MsoNormal
style="BORDER-RIGHT: medium none; PADDING-RIGHT: 0in; BORDER-TOP: medium none; PADDING-LEFT: 0in; PADDING-BOTTOM: 0in; MARGIN: 0in 0in 0pt; BORDER-LEFT: medium none; PADDING-TOP: 0in; BORDER-BOTTOM: medium none; mso-border-bottom-alt: double windowtext 2.25pt; mso-padding-alt: 0in 0in 1.0pt 0in"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana"><o:p> </o:p></SPAN></P></DIV>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana"><o:p> </o:p></SPAN></P>
<DIV
style="BORDER-RIGHT: medium none; PADDING-RIGHT: 0in; BORDER-TOP: medium none; PADDING-LEFT: 0in; PADDING-BOTTOM: 1pt; BORDER-LEFT: medium none; PADDING-TOP: 0in; BORDER-BOTTOM: windowtext 2.25pt double">
<P class=MsoNormal
style="BORDER-RIGHT: medium none; PADDING-RIGHT: 0in; BORDER-TOP: medium none; PADDING-LEFT: 0in; PADDING-BOTTOM: 0in; MARGIN: 0in 0in 0pt; BORDER-LEFT: medium none; PADDING-TOP: 0in; BORDER-BOTTOM: medium none; mso-border-bottom-alt: double windowtext 2.25pt; mso-padding-alt: 0in 0in 1.0pt 0in"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana">In conjunction with the
"Sequencing the Maize Genome" project we have created a website for the general
public (<A href="http://www.maizegenome.org/">www.maizegenome.org</A>) which
aims to provide information and updates relating to active maize genom<SPAN
class=400340818-14082003>e</SPAN> sequencing projects. <SPAN
style="mso-spacerun: yes"> </SPAN><o:p></o:p></SPAN></P>
<P class=MsoNormal
style="BORDER-RIGHT: medium none; PADDING-RIGHT: 0in; BORDER-TOP: medium none; PADDING-LEFT: 0in; PADDING-BOTTOM: 0in; MARGIN: 0in 0in 0pt; BORDER-LEFT: medium none; PADDING-TOP: 0in; BORDER-BOTTOM: medium none; mso-border-bottom-alt: double windowtext 2.25pt; mso-padding-alt: 0in 0in 1.0pt 0in"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana"><SPAN
style="mso-spacerun: yes"> </SPAN><o:p></o:p></SPAN></P></DIV>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana"><o:p> </o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana">We are constantly searching for
ways to improve our website<SPAN class=400340818-14082003>s</SPAN> and to make
the data <SPAN class=400340818-14082003>generated by this </SPAN>project
easily accessible and informative to the maize <SPAN
class=400340818-14082003>research </SPAN>community. As always, we welcome your
feedback -- please e-mail us at <A
href="http://www.tigr.org/tdb/tgi/maize/">http://www.tigr.org/tdb/tgi/maize/</A>.<o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana"><o:p> </o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana"><o:p> </o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana">Cathy Whitelaw (The Institute for
Genomic Research)<o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana">Brad Barbazuk
(</SPAN><?xml:namespace prefix = st1 ns =
"urn:schemas-microsoft-com:office:smarttags" /><st1:place><st1:PlaceName><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana">Donald</SPAN></st1:PlaceName><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana"> </SPAN><st1:PlaceName><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana">Danforth</SPAN></st1:PlaceName><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana"> </SPAN><st1:PlaceName><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana">Plant</SPAN></st1:PlaceName><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana"> </SPAN><st1:PlaceName><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana">Science</SPAN></st1:PlaceName><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana"> </SPAN><st1:PlaceType><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana">Center</SPAN></st1:PlaceType></st1:place><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana">)<o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana"><o:p> </o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana">This project is supported by NSF
Plant Genome award, DBI-0221536 <o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana"><o:p> </o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana"><o:p> </o:p></SPAN></P></FONT></DIV></BODY></HTML>