GDR Newsletter August 2005
Welcome to the third 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/newsletter0705.shtml
Attached is the pdf version of this newsletter.
What's new at GDR?
1. GDR web address change
2. Updates to peach transcriptome map
3. Anchored genes and ESTs are displayed in genetic maps in CMap
4. New EST data
5. Run InterProScan directly from the EST detail page
6. Bulk search and download feature available in the EST search pages.
7. Abstracts and powerpoint presentations of NRI funded projects available
Community News
1. International Symposium on Biotechnology of Temperate Fruit Crops and
Tropical Species, Daytona Beach, FL USA, October 10-14, 2005
2. Fruit and Nut Workshop, Saturday January 14, 8 am-12 pm. Plant and
Animal Genome Conference XIV, San Diego, January 14-18, 2006. Conference
organizer, Dr Amy Iezzoni.
3. 3rd International Rosaceae Genomics Conference in Napier, New Zealand,
March 19-23, 2006
What's new at GDR?
1. GDR web address change.
GDR is now accessible at the following URL: http://www.rosaceae.org. At
the current time this URL will be redirected to
http://www.mainlab.clemson.edu/gdr while we move the database over to the
new web address. In all future web references to GDR please use the
http://www.rosaceae.org URL.
2. Updates to peach transcriptome map.
Unique peach ESTs are being hybridized to peach BACs to map the ESTs onto
the genetically anchored peach physical map. 569 peach unigenes are
anchored to various Rosaceae genetic maps. 367 of them are anchored by
direct hybridization to genetically anchored BACs and the rest (202) are
anchored by hybridization to BACs that belong to genetically anchored BAC
contigs. 375 unigenes are anchored to the TxE map. GDR map viewer and the
downloadable peach transcriptome data reflects the updated peach
transcriptome map.
3. Anchored genes and ESTs are displayed in genetic maps in CMap.
The 25 major genes affecting agronomic characters, anchored to TxE map
(Dirlewanger et al, 2004), are now displayed in TxE map in CMap.The peach
ESTs are also displayed by the markers with which they share BACs or BAC
contigs in hybridization in eight Prunus genetic maps. The anchored ESTs
and markers in CMap are linked to GDR detail pages. View an example CMap
page.
4. New EST data
A new peach EST dataset sequenced by Elisa Vendramin from the CRA Istituto
Sperimentale per la Frutticoltura is now publicly available. A total of
1667 clones from peach fruit mesocarp have been analyzed. Assembly of
these ESTs produced 1116 putative peach unigenes within this dataset.
5. Run protein motif and domain searches using InterProScan.
Users can now search ESTs against the European Bioinformatics Institutes
InterPro database directly from GDR. InterPro is a database of protein
families, domains and functional sites in which identifiable features
found in known proteins can be applied to translated ESTs. Finding
functional domains in a EST may corroborate the putative function obtained
by sequence homology or provide more information for ESTs with no homology
to other known proteins. Our site programmatically accesses EBI's
InterProScan so users can query InterPro without uploading EST sequences
at the EBI's site. To access an example EST page, go to
(http://www.mainlab.clemson.edu/java/gdr/EST.jsp?
CloneName_Result=PP_LEa0002H11f)
and run InterProScan.
6. Bulk search and download feature available in the EST search pages.
A bulk search is available for peach, almond, strawberry, and GenBank
rosaceae EST datasets. Users can upload a file with multiple clone names
or Genbank accession numbers and have returned to them all the sequence
and homology information
associated with those sequences. Any bulk EST search query will now return
downloadable files of fasta formatted sequence and homology results.
7. Abstracts and powerpoint presentations of NRI funded projects.
View and download all the abstracts and powerpoint presentations of the
NRI funded projects presented at the recent ASHS meeting. Many thanks to
the authors and Dr Ed Kaleiko for providing us with this information.
Subscription
Visit our mailing list site at GDR to be added/removed to the mailing
list. http://www.mainlab.clemson.edu/gdr/MailingList.shtml
Work in progress
Processing new peach shoot ESTs, rose ESTs from vegetative apices and
apices at floral transition and blackberry ESTs
Extending the gene and QTL data available in CMap.
Integrating data from the USDA CSREES NRI projects
Developing a rosaceae EST unigene v2 with enhanced annotation
