Welcome to the first issue of the GDR newsletter. This newsletter will be
issued quarterly to inform users about new or updated data and features in
GDR and community related news. Please feel free to provide feedback and
news either directly by email or via our online form.
The online version can be found at
http://www.genome.clemson.edu/gdr/newsletter.shtml.
Attached is the pdf version of this newsletter.
Whats new at GDR?
1. Updates to peach physical map
2. Updates to peach transcriptome map
3. CMap, the comparative map viewer, now available
4. Updates to Rosaceae genetic map data
5. Strawberry EST data are added to GDR
6. Genbank Rosaceae and genera EST assemblies available
7. Data Overview pages are available
8. New Publication search tool is available
9. Navigation bar modified
10. New analysis tool, CAP3 Assembly Server, is available
11. GDR Tutorial is available
12. Fruit Tree Genomics Workshop summary document available
13. GDR published in BMC Bioinformatics
14. GDR presentation at PAG-XIII
15. Enhanced computational resources
1. Updates to the peach physical map
The Peach physical map now contains 1223 contigs and 16879 BACs. 134
contigs are anchored to TxE, the Prunus reference map. The current
physical map data was generated from an FPC assembly done on October 13,
2004. The next updated version of the physical map will be available at
the end of January, 2005. WebFPC/WebChrom displays the peach physical map.
2. Updates to the peach transcriptome map
Unique peach ESTs are being hybridized to peach BACs to map the ESTs onto
the genetically anchored peach physical map. 294 peach unigenes are
anchored to various Rosaceae genetic maps by direct hybridization to
genetically anchored BACs. 163 unigenes are anchored to the TxE map. An
additional 277 peach unigenes are anchored to genetic maps by
hybridization to BACs that belong to genetically anchored BAC contigs.
The GDR map viewer displays the updated TxE map with the associated
transcriptome map.
3. CMap, the comparative map viewer, now available
CMap, a web-based tool that allows users to view comparisons of maps from
various species, is implemented at GDR. In this release, we present nine
Rosaceae genetic maps. Thanks to all the authors who assisted GDR team for
uploading their mapping data.
4. Updates to Rosaceae genetic map data
Nine Rosaceae genetic maps are available through CMap, the comparative map
viewer. A total of 872 genetic markers from 11 Rosaceae genetic maps are
available from the marker search page.
5. Strawberry EST data processed through GDR
Over 1800 high quality ESTs from octoploid strawberries (Fragaria x.
ananassa) have been annotated and added to GDR. The annotation includes
sequence assembly, homology search and SSR mining. Detailed description of
the project, sequences, and the annotation results can be searched,
browsed and downloaded from the data overview page and EST search site.
Thanks to Dr. Kevin Folta at University of Florida for submitting his
sequences for processing through the GDR. If you would like to have your
sequences processed through the GDR pipeline please contact
dorrie(a)genome.clemson.edu.
6. Genbank Rosaceae and genera EST assemblies available
All the publicly available Rosaceae ESTs have been assembled using CAP3.
Assemblies were also generated for the EST sets of each genus - Malus,
Prunus, Fragaria, Rosa and Pyrus. The contigs and singlets for each
assembly have bee searched against the Swissprot database and the homology
results are available to browse and download in the data overview page.
Homology with the NCBI nr protein database and other rosaceae ESTs will be
available soon.
7. Data Overview pages are available
Data Overview pages are available. For EST projects, users can browse and
download the detailed project description and the annotated sequence data.
8. New Publication search tool is available
GDR introduces a publication search tool where users can perform Boolean
searches by title, author, keyword and publication year. The GDR stores
publications from Pubmed that satisfy the following Boolean expression:
(Rosaceae OR Prunus OR Rosa OR Fragaria OR Pyrus OR Malus) AND (gene OR
genome OR map OR ssr OR microsatellite OR annotation OR est OR marker OR
sequence). Relevant publications from sources other than Pubmed may be
included.
9. Navigation bar modified
GDR has implemented a new navigation bar on top of each page to allow
organized and quick access to major features of GDR. Major headings
include about us, map resources, search, tools and Rosaceae resources.
Each heading has a dropdown menu for a quick access to various pages.
10. New analysis tool, CAP3 Assembly Server, is available
GDR has implemented a new analysis tool, the CAP3 assembly server, in
addition to the FASTA and BLAST servers. GDR also has links to various
useful remote analysis tools.
11. GDR Tutorial is available
GDR overview and mapping resources tutorials are now available. Tutorials
for search tools and analysis tools will be available soon.
12. Fruit Tree Genomics Workshop summary document available
Download the summary report from the October 2004 Technology Roadmap
Temperate Fruit Genomics, Genetics and Breeding Workshop at Baltimore,
Maryland.
13. GDR published in BMC Bioinformatics
GDR (Genome Database for Rosaceae): integrated web resources for Rosaceae
genomics and genetics research. BMC Bioinformatics. 2004; 5: 130
(Abstract|PDF)
14. GDR presentation at PAG-XIII
GDR poster presentation at PAG-XIII, January 15-19, 2005.
P830: Genome Database For Rosaceae (GDR)
15. Enhanced Computational Resources
In January 2005, Clemson University purchases a 32 node apple grid to
enhance the computational infrastructure of the CUGI Bioinformatics
Center. This equipment will help ensure that data analysis in GDR remains
current and readily available to the Rosaceae community.
Subscription
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Work in progress
1. Processing new peach shoot ESTs and rose ESTs from vegetative apices
and apices at floral transition
2. New comprehensive EST search site: Search by putative function from
tissue, sequence homology and anchored map position will be available in
addition to current search categories.
3. EST search results site with bulk download feature: Sequences in Fasta
format and homology results for the EST search result sets can be
downloaded.
4. Tutorials for search and analysis tools.
