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3rd International Rosaceae Genomics Conference - Pre-Conference Workshop

by Neill & Sue Page

Hello everyone, In addition to the RGC3 conference in Napier, a pre-conference workshop will be held in Auckland, 13-17 March 2006. The call for application this workshop was originally 15 October 2005 but is now being extended to 15 November 2005. Please pass the information to any graduate student / young researcher / colleague who may be interested in attending this workshop. A description of the workshop is available on the RCG3 website, www.rgc3.co.nz. Best regards David Chagne Pre-conference Workshop organiser

19 years, 7 months

3rd International Rosaceae Genomics Conference - March 2006

by Neill & Sue Page

Hello everyone We are pleased to announce that the registration information is now available on our website http://www.rgc3.co.nz Please pass this information on to any colleagues who may be interested in attending this conference. Please read all the information carefully before commencing the registration process. To register online - you will need to complete the online registration form, submit this, then you will be taken to a secure site to process the payment for the registration fee and any activities you select. Alternatively you can download the registration form from the Registration Page and either send in by mail or fax through. If you have any queries please do not hesitate to contact us. REMINDER - that abstract titles are due in by 31 October 2005. As you will see from the website the programme and activites are exciting and we are looking forward to an excellent conference and meeting you there. Regards Sue Page Conference Organiser Encore Events Management Ltd 13a Charles Street Napier, New Zealand Ph/Fax: + 64 (06)835 9549 Mobile: + 64 027 669 1345 Email: encore.events(a)clear.net.nz

19 years, 7 months

GDR newsletter August 2005

by Sook Jung

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

19 years, 8 months

3rd International Rosaceae Genomics Conference

by Neill & Sue Page

Dear All We wish to advise that the website for the above conference, www.rgc3.co.nz, has now been updated to include the latest programme and Call for Papers. Please visit the site and complete the pre-registration form if you have not already done so. We will keep you informed as new information is loaded onto the website. 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

19 years, 10 months

GDR newsletter April 2005

by Sook Jung

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.

20 years

3rd International Rosaceae Geonomis Conference

by Neill & Sue Page

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

20 years, 1 month

Mailing List Name Change

by Stephen Ficklin

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/

20 years, 3 months

GDR newsletter January 2005

by Sook Jung

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.

20 years, 4 months

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