Announcement from the Consortium for Maize Genomics

Whitelaw, Cathy A. whitelaw at tigr.org
Fri Aug 15 14:30:19 EST 2003


Dear Colleagues,

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 http://www.tigr.org/tdb/tgi/maize/.

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).

For Release 2.0 assembly statistics summary, please visit: 
http://www.tigr.org/tdb/tgi/maize/release2.0/assembly_summary.shtml


For Sequencing progress to date, please visit:

http://www.tigr.org/tdb/tgi/maize/progress_graph.shtml


For Analysis of repetitive sequences in the maize genomic assemblies, 
please visit: 
http://www.tigr.org/tdb/tgi/maize/release2.0/repeat_analysis.shtml

For Gene matches to maize genomic sequences, please visit:

http://www.tigr.org/tdb/tgi/maize/release2.0/gene_matches.shtml

For Mapping maize assemblies to maize sequence markers, please visit:

http://www.tigr.org/tigr-scripts/tgi/marker2.annotator.pl?species=combo_marker

In addition to the Release 2.0 data and BLAST server, we have added 
several new features to our website:

---GENOME MAP BROWSER---

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'.  The 
genome map browser provides links between maize sequence markers, 
maize tentative consensus (TC) sequences from the TIGR Maize Gene 
Index (http://www.tigr.org/tdb/tgi/zmgi/), maize genomic assemblies 
(AZMs for Assembled Zea mays) and maize BAC contigs.  The genome map 
browser is located at: 
http://www.tigr.org/tigr-scripts/tgi/print_chromosomes.pl
and was built using tools provided by the Generic Model Organism 
Database Project (http://www.gmod.org/).

---BAC VIEWER---

We took all maize genomic sequences >10 kb from GenBank and searched 
against our maize AZMs using BLAT.  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.  The BAC viewer is located at 
http://www.tigr.org/tigr-scripts/tgi/BAC.annotator.pl and was built 
using tools provided by the Generic Model Organism Database Project 
(http://www.gmod.org/).

---BAC ANNOTATION---

We took all maize genomic sequences > 10 kb from GenBank and 
processed them using the Eukaryotic Genome Control automated 
annotation pipeline at TIGR.  The annotation results are available 
at: 
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&amp;data=BAC> 
.  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.

---MAIZE REPEAT DATABASE---

We have compiled a database of maize repetitive sequences which is 
available for download.  Please visit the following link for more 
information: http://www.tigr.org/tdb/tgi/maize/repeat_db.shtml

---GENE ONTOLOGY ASSIGNMENTS---

We have made automated Gene Ontology assignments to the AZMs from the 
MF and HC combined assembly, based on significant hits to proteins 
with an existing GO assignment.

http://www.tigr.org/tdb/tgi/maize/release2.0/GO/GO.html

In conjunction with the "Sequencing the Maize Genome" project we have 
created a website for the general public (www.maizegenome.org 
<http://www.maizegenome.org/> ) which aims to provide information and 
updates relating to active maize genome sequencing projects.  

We are constantly searching for ways to improve our websites and to 
make the data generated by this project easily accessible and 
informative to the maize research community. As always, we welcome 
your feedback -- please e-mail us at maize at tigr.org.

Cathy Whitelaw (The Institute for Genomic Research)
Brad Barbazuk (Donald Danforth Plant Science Center)

This project is supported by NSF Plant Genome award, DBI-0221536





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