GDR Newsletter April 2005
Welcome to the second issue of the GDR newsletter. This newsletter is
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.mainlab.clemson.edu/gdr/newsletter0405.shtml
Attached is the pdf version of this newsletter.
Community News
1. View the projects funded through the 2004 USDA CSREES National
Research Initiative.
2. Announcing 3rd International Rosaceae Genomics Conference in
Napier, New Zealand, March 19-23, 2006
3. Rosaceae workshop to be held at the ASHS Annual Meeting in Las
Vegas, NV, July 18-21, 2005
4. Download the notes from the 2005 Fruit and Nut Workshop at the
Plant and Animal Genome Conference
What's new at GDR?
1. Updates to peach physical map
2. Updates to CMap
3. Updates to Genbank Rosaceae EST data
4. Advanced EST search page available
5. Download/view transcriptome data
6. New feature in EST data page
7. Community page available
8. New online analysis tool, SSR server, is available
9. GDR Message Board available
10. GDR web address is changed
1. Updates to the peach physical map
The latest peach physical map contains 16895 BACs 1388 contigs. A
total of 152 contigs are anchored to the TxE map, the Prunus reference
map. The current physical map data was generated from an FPC assembly
done on January 6, 2004. WebFPC/WebChrom displays the peach physical
map.
2. Updates to CMap
19 Rosaceae genetic maps are available through CMap, the comparative
map viewer. Recent addition includes seven apple maps and two cherry
maps archived from RoseDB by Anjela Baldo at USDA, ARS PGRU and peach
PMP2 map.
3. Updates to GenBank Rosaceae EST data
GenBank Rosaceae EST data have been annotated by sequence homology
analyses against SwissProt database in addition to GenBank nr protein
database.
4. Advanced EST search page available
A new comprehensive EST search page is available for the EST datasets.
Users can search ESTs in any combination of clone name, organism
(genus, species), tissue type, putative function or species of the
homologs, and anchored map position where relevant. The search results
site has an option for downloading the sequences in fasta format.
5. Download/view transcriptome data
The peach transcriptome page provides the current status of the peach
transcriptome map and links to an Excel spreadsheet with transcriptome
map data detail and other relevant resources.
6. New feature in EST data page
A new option, "Printable Data" is available in the EST data page to
present all the EST data in one page. View an example page.
7. Community page available
Visit our community page for conference news, information on our
outreach program and other community resources such as a list of the
thirteen projects funded through the 2004 USDA CSREES National
Research Initiative: Plant Genome, Bioinformatics, and Genetic
Resources.
8. New online analysis tool, SSR server, is available
GDR has implemented a new analysis tool, the SSR server. Using this
online tool users can upload a batch file of sequences and have
summary, individual and fasta formatted library file of the SSR
containing sequences returned. The SSR server joins the growing list
of online GDR tools such as the CAP3 assembly, FASTA and BLAST
servers.
9. Searchable archives of GDR Message Board available
Users can view the searchable archives from the gdr mailing list. If
you are a registered gdr user you can use the GDR email mailing list
gdr-list(a)genome.clemson.edu to send out community based information or
requests from your own computer. These emails will automatically be
archived onto the message board where they can be searched by subject,
thread, author or date.
10. GDR web address is changed.
GDR web address is now http://www.mainlab.clemson.edu/gdr/. The old
address will be automatically redirected to the new address.
Subscription
Visit our mailing list site at GDR to be added/removed to the mailing
list. http://www.genome.clemson.edu/gdr/MailingList.shtml
Work in progress
1. Processing new peach shoot ESTs and rose ESTs from vegetative
apices and apices at floral transition
2. EST search by uploading a list of clone names/accession numbers
3. EST search results site with bulk download feature: Excel files
with sequence homology data for the EST search result sets can be
downloaded.
4. Development of an online sequence processing tool where users can
upload their sequence files (trace or seq and qual files) and have the
high quality sequences returned. These in turn can be assembled using
the existing CAP3 assembly tool, mined for SSRs using the SSR server
and then searched against known plant proteins or rosaceae ESTs using
the FASTA and BLAST servers.
5. Tutorials for search and analysis tools
6. Addition of more mapping data.
Dear All
Please find attached the First Announcement for the 3rd International
Rosaceae Geonomics Conference which is being held in Napier, New Zealand
19-22 March 2006.
Please feel free to forward/distribute this announcement to anyone that you
feel may be interested in attending this conference.
The website www.rgc3.co.nz is operational and you can complete the
pre-registration form online or print out the attached and fax back or send
by mail.
If you have any queries please do not hesitate to contact me.
Regards Sue Page
Conference Organiser
Encore Events Management Ltd
13a Charles Street
Napier, New Zealand
Ph/Fax: (06)835 9549
Mobile: 027 669 1345
Email: encore.events(a)clear.net.nz
The global mailing list for GDR research collaboration has changed names.
It is now: GDR-LIST(a)genome.clemson.edu
The GDR mailing list currently consists of over 160 email addresses of
researchers from all over the world involved with the development of the
Genomic Database for Rosaceae. Anyone who is a member of the GDR mailing
list may post messages to the group by sending emails to:
GDR-LIST(a)genome.clemson.edu
If you wish to unsubscribe please visit our web site here:
http://www.genome.clemson.edu/gdr/MailingList.shtml
Regards,
Stephen Ficklin
--
Systems Programmer
Clemson University Genomics Institute
300 BRC, Clemson University
(864) 656-4643
http://www.genome.clemson.edu/
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
Visit our mailing list site at GDR to be added/removed to the mailing list.
http://www.genome.clemson.edu/gdr/MailingList.shtml
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.
