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&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
