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MGOS History
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A new BioMart style interface for the Genes and EST Contigs queries is now available.
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A link to all abstracts from the 4th IRBC conference held Oct. 9-14, 2007 is now available from the home page.
We would also like to add photos from the conference, so please send us any photos that you would like to share on the website.
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Community annotation now available. This includes the gene name and
description, transcript structure and location, gene ontology terms,
fungal anatomy terms, publication information, and name of the person
making the annotation submission.
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Updated Magnaporthe grisea annotations.
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Converted to TIGR rice pseudomoledules and updated annotation.
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Added MGOS forum. This forum allows participants to post topics of interest
and provides a mechanism to communicate with the Magnaporthe grisea community and
the MGOS project team.
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A few releases ago, we added the UniProt rice proteins and the Genbank M.grisea proteins, but its taken us a few releases to get it right. This is the final state: (1) All UniProt rice proteins except Hypothetical and all Genbank M.grisea proteins are in MGOS. (2) These are used in computing the AGCoL gene models. If a protein does not align to the genome, it is put on the virtual chromosome 0. (3) Improved alignments of the proteins to the genome. (4) You can use alternative names in the Basic Gene Search.
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Update with the latest Broad Institute Release 5 (Jan 2006) M.grisea genomic sequence. Replace the R4 genes with the R5 genes.
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The PAVE algorithm has been optimized to increase the number of mate pairs in a contig and decrease the number of redundant contigs. Both the rice and M. grisea EST assemblies have been updated.
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The genes have been recomputed and renamed. The rice genes prefix with MOSa and the M. grisea prefix with MMGa.
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The secreted proteins have been blasted against the new AGCoL M.grisea genes since their mapping to the old M.grisea R4 genes was out-of-date (29 did not match and are not in the database).
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The Agilent Probe Id is used in place of the Systemic name.
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We have done a lot of cleanup to remove every little bug. If you find a problem, please let us know by entering the problem in the 'comments and question' form at the bottom of each page.
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Update with the IRGSP V4 genome sequence, the latest TC sequences, and new AGCoL consensus genes.
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Data submission: On the Gene page, there is a 'Submit Annotation" in which you can
submit changes for any MGOS gene. Once submitted, it is emailed to Dan Ebbole for approval.
All approved changes will be listed on their respective gene page, and on the 'Browse Submitted
Annotation' page.
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Mutant Recovery: A number of the mutants have gene recovery results. These are accessible
from the 'Browse Mutant Recovery' link on the mutant page.
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New microrray: A microarray experiment performed by Ralph Dean et al. has been downloaded from GEO
and entered into MGOS. Not all of the design details are available since they were not
in GEO. The experiment can be viewed from the Microarray "Browse Experiment" page.
The results are also shown on each Gene page if the microarray probe matches the sequence
of the gene.
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UniProt Rice Annotated Genes: We were using BLASTP to align the UniProt rice genes to
the rice sequence, and taking
the highest hit. But this meant that generally only one exon was covered. Moreover, we
were using all the UniProt rice genes. This release: (1) We are only using the UniProt
rice genes that are 'annotated'. (2) We have developed an algorithm to align the protein
sequence to the genome using all the neighboring BLASTP HSPs. (3) If a UniProt rice
gene does not have a good alignment to the rice sequence, it is given an AGCoL gene name
and added to the AGCoL gene list so that it can be queried. (4) The UniProt rice genes
are used in the AGCoL consensus gene algorithm.
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Main pages have been re-formated in order to make the "Advanced Search" more obvious.
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New rice EST assembly and new AGCoL gene models.
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If a EST contig or FL-cDNA does not align to the rice genome, it is assigned is given an
AGCoL gene name and added to the gene list. These can be searched from the Gene page
by selecting chromosome 0.
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In order for users to be able to search the gene pages based on the canonical name,
we have downloaded all Magnaprothe genes from Genbank, and used all rice genes from
Uniprot, and entered them into MGOS. All names that were in the Genbank/Uniprot
records are also listed as synomyous names for the gene, and can be used in searches.
We invite user feedback as to whether we are supplying the right names needed by
the community.
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Enhanced search capabilities for the Gene, EST Contig and Sage page.
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For PIs only: the microarray submission page has been redone for ease of use.
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Using the IRGSP V3 genome sequence. As there were too many changes between V2 and V3,
we could not continue to map the original AGCoL gene names to the new AGCoL consensus
genes, hence, the naming is new.
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All pages have been given the same look and feel. The EST, SAGE and Gene page
all have similar queries, where possible.
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The previous release was based on the TIGR pseudomolecules of the IRGSP sequence.
This release is based on the IRGSP V2 pseudomolecules. Our algorithm for determining
the consensus genes based on all evidence was rerun on the new pseudomolecules.
The gene names from the orginal set (based on TIGR pseudomolecules) where mapped
to the new consensus genes so that gene names would be preserved as much as possible.
Under the gene page, there is a list of genes that no longer exist, and a list of
genes that are new.
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All EST contigs and AGCoL genes are blasted against UniProt and the best match is
displayed with the record. (Previously, we were using SwissProt).
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The user has a choice between the CGI based Genome browser or a Java based Genome
browser interface. The Java interface was developed by AGCoL and supported in part
by this grant.
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The secreted proteins provided by Dan Ebbole now have a track in the MG genome browser.
The Genbank/UniProt genes for MG/rice now have a track in the genome browser.
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The SAGE data has been added.
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The EST has changed from running only CAP3 to using the TGICL followed by CAP3,
and then our PAVE postprocessor to merge and split contigs based on mate pairs.
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We developed an algorithm to determine the best gene models from all other evidence.
The resulting genes are called the AGCoL genes. The Gene Pages contain an entry for
each AGCoL gene.
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Everything has help and information
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