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
