| News archive |
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New web services available for GabiPD (30-AUG-10)
•Three new web services are available in GabiPD. These can be accessed by the BioMoby Dashboard, the Taverna client, by a selfmade Perl/Java client or on the command line.
• More infomration in our WebServices project page.
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About 30.000 GSS sequences from sugar beet are publicly available (01-AUG-10)
• These 30.022 GSS (BAC ends) from the sugar beet DH line KWS2320 were generated in the GABI-BPM project and are publicly available via GabiPD and GenBank.
• Please find the data via GreenCards searching for "IGS-SCF-0106*". |
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Merged Arabidopsis SNPs downloadable (13-JUL-10)
•Merged SNP data from three genome-wide natural variation studies in A. thaliana (Nordborg et al., 2005; Clark et al., 2007; Ossowski et al., 2008) are now downloadable.
•A related GabiPD publication on the influence of these SNPs on Arabidopsis thaliana phosphorylation patterns appeared recently in BMC Genomics (Riano-Pachon et al., 2010)
Download SNPs |
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Genome annotation for Poplar (black cottonwood) integrated in GabiPD (12-JUL-10)
•Populus trichocarpa genome annotation v2.0 from Phytozome v5.0 was integrated into GabiPD, including gene structures, and protein domains.
•Please find the data via GreenCards with the keyword "POPTR*".
•Gene structures and domains are visualized in the cDNA display of every Gene GreenCard.
View example
•Orthologous protein coding genes where identified, using InParanoid v4.1, between Chlamydomonas reinhardtii (JGI 3.1), Rice (MSU 6.1), Arabidopsis (TAIR9.0) and Poplar (Phytozome2.0) |
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About 30.000 GSS sequences from sugar beet are available (03-MAY-10)
• These 30.022 GSS (BAC ends) from the sugar beet DH line KWS2320 were generated in the GABI-BPM project and are exclusively available for all WPG-participants.
• Please find the data via GreenCards searching for "IGS-SCF-0106*". |
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BLAST searches for all GabiPD sequences against GenBank (23-APR-10)
•All sequences in GabiPD have been similarity-based mapped to GenBank sequences. Results are available through GreenCards. |
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Updated genome annotations for Arabidopsis and Rice (10-MAR-10)
•Arabidopsis thaliana TAIR 9.0 and Oryza sativa ssp. japonica MSU 6.1 where integrated into GabiPD, including gene structures and Gene Ontology.
•Gene structures are visualized in the cDNA display of every Gene GreenCard.
View example (Rice) |
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New SATlotyper version available (05-MAR-10)
• Version 0.1.4 of SATlotyper is now available with better SAT solving support for windows.
Download |
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Barley and Arabidopsis Affymetrix chip target sequences mapped to related cDNAs (23-FEB-10)
•All Barley (Affymetrix chip Barley1) and Arabidopsis (ATH1-121501) probesets (target sequences) have been similarity-based mapped to Rice (MSU 6.1) and Arabidopsis (TAIR 9.0) cDNAs annotated in the respective genome projects.
View example (Rice) |
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Short reads from 2000 BACs and individual barley chromosomes are exclusively available for WPG members (01-FEB-10)
• Short reads, obtained using 454 technology, from Barley individual chromosomes and 2000 BACs, generated within the GABI-BARLEX project at IPK are exclusively available for WPG members in our Download page, search for GABI-BARLEX. |
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Short reads from Barley Chromosome 1H are publicly available (21-JAN-10)
• Short reads, obtained using 454 technology, from Barely chromosome 1H generated within the GABI-BARLEX project at IPK are publicly available in our Download page, search for GABI-BARLEX.
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All GabiPD clones similarity-based mapped to up-to-date database versions (11-JAN-10)
•All clone sequences in GabiPD have been similarity-based mapped to NCBI's UniGenes(Dec2009), UniProt v15.12 (UniRef100), Arabidopsis TAIR9 and Rice MSU6.1.
• Results are available in every clone GreenCard in the section 'View Blast Searches', and 'Related with'.
View example (Arabidopsis)
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Partial sequences of 2000 BAC clones from Hordeum vulgare cultivar Morex exclusively available for WPG participants (11-JAN-10)
• Sequences were generated using 454 technology within the GABI-BARLEX project at IPK.
• Please find the data via GreenCards with the keyword "HVVMRXALL*". |
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Arabidopsis thaliana SNPs mapping onto cDNAs integrated in GabiPD (24-DEC-09)
•Single nucleotide polymorphisms from three genome-wide natural variation studies (Nordborg et al., 2005; Clark et al., 2007; Ossowski et al., 2008) were mapped onto the Arabidopsis thaliana genome annotation (release TAIR7.0) and are available through Gene GreenCards
• Example At1g01010.1. |
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Download annotated 2DE gels images in SVG format (01-DEC-09)
• 2DE gel images can now be downloaded in Scalable Vector Graphics (SVG) format and visualized in supporting web browsers (preferred way, e.g., Firefox or Safari) or standalone software, e.g., Inkscape.
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Partial sequences of 91 BAC clones from Hordeum vulgare cultivar Morex are publicly available (19-NOV-09)
• Sequences were generated using 454 technology within the GABI-BARLEX project at IPK.
• Please find the data via GreenCards with the keyword "HVVMRXALLhA*". |
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Arabidopsis candidate substrates of protein kinases downloadable (06-NOV-09)
•The list of candidate substrates of Arabidopsis protein kinases was extended and is accessible via our Plant phosphoproteomics page.
•You can download the complete list from the Download page.
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New MapMen Site of Analysis developed (04-NOV-09)
•The new MapMen Site of Analysis developed in the scope of the GABI-MapMen project is accessible via GabiPD's Project page.
•You will find MapManWeb via the WebTools
• Download the recent MapMan desktop version.
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Chlamydomonas reinhardtii genome annotation integrated in GabiPD (15-OCT-09)
•The genome annotation (JGI v3.1) of the green algae C. reinhardtii was integrated into GabiPD in colaboration with GoFORSYS.
• Please find the data via GreenCards with the keyword "CRE3*". |
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New download for potato BAC sequences (15-SEP-09)
•All potato BAC sequences are now downloadable via PoMaMo. Go to "PoMaMo sequences".
Go to PoMaMo |
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New Potato BAC sequences publicly available (17-AUG-09)
• New BAC sequences (assembled) were integrated in PoMaMo. The data were generated in the GABI-CONQUEST project.
• You can search for the sequences using the clone name (BA111o5, BA132h9, BC93c12, BC136j5).
• All previously integrated BAC sequences (assembled) are now publicly available and accessible via the physical maps in PoMaMo or searchable using the clone name.
Go to PoMaMo |
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New Login mechanism and menu layout in GabiPD (24-JUN-09)
• From now on you will find a "Login" link to the login page in the top-right corner of the site. This makes it unobtrusive for new users of GabiPD, while keeping the functionality for existing users.
• We made some changes in the design of the menu column, we hope you find it pleasing and useful. |
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Updated Barley BAC assemblies are exclusively available for WPG participants (23-JUN-09)
• Partial sequence assemblies of 91 BAC clones from Hordeum vulgare cultivar Morex were updated by the IPK. Sequences were generated using 454 technology within the GABI-BARLEX project.
• Please find the data via GreenCards with the keyword "HVVMRXALLhA*". |
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New MapMan Release 3.0.0 available (22-JUN-09)
New Features and Fixes:
• Simultaneous visualization of multiple assays
• Exportable table based displays of mapped data
• Fixes MS Windows Vista issues
(Download MapMan 3.0.0) |
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New SATlotyper version available (15-JUN-09)
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Version 0.1.3 of SATlotyper is now available.
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SNP sites of the form "ACNN" (see example4.csv) can be handled now (where N = not known).
Download |
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Potato physical maps are now publicly available in PoMaMo (09-JUN-09)
•Potato physical maps and a BAC assembly for chromosome 5 are now publicly accessible via PoMaMo, The Potato Maps and More Database.
•The data were generated in the scope of GABI-CONQUEST. A related publication appeared recently in Theoretical and Applied Genetics (U. Achenbach et al. 2009).
View mapping data. |
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Barley gene expression data publicly available (22-MAY-09)
•Barley gene expression data (Barley1 Affymetrix array) generated in the scope of GABI-SEED II, GABI-MALT and GABI-MapMan (N. Sreenivasulu et al. 2008) is available for visualization using MapManWeb.
•All Barley probesets have been integrated in GabiPD, including target sequences and oligonucleotides as well as functional annotation (gene ontology and MapMan) and results of similarity-based mapping to Rice genes.
View example |
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New plant phosphoproteomics page in GabiPD (25-MAR-09)
•This page provides references to plant phosphosite databases and information on in vitro substrates of Arabidopsis MAP kinases including results from GABI-LAPP.
•Proteomic and bioinformatic approaches to investigate plant protein phosphorylation have been reviewed recently (B. Kersten et al. 2009).
• View phosphoproteomic page
•View At Gene GreenCard with integrated kinase information |
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Barley gene expression data exclusively available for WPG participants (12-FEB-09)
•Barley gene expression data (Barley1 Affymetrix array) generated in the scope of GABI-SEED II, GABI-MALT and GABI-MapMan (N. Sreenivasulu et al. 2008) is available for visualization using MapManWeb.
•All Barley probesets have been integrated in GabiPD, including target sequences and oligonucleotides as well as functional annotation (gene ontology and MapMan) and results of similarity-based mapping to Rice genes.
View example |
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Potato SNP data from 21 loci are now public available (20-JAN-09)
•The data were generated in the scope of the GABI-CONQUEST-2 project aiming at the identification of genes and their SNPs, which control field resistance to late blight.
•The major association with resistance to late blight was found at the StAOS2 locus (K. Pajerowska-Mukhtar et al. 2009).
•Please seach GreenCards using the locus name as a key word, e.g. 'StAOS2*'.
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Update on the Gene GreenCards for Oryza sativa ssp. japonica. (15-JAN-09)
• The Rice Gene GreenCards now display graphically the gene structure on the cDNA like for A. thaliana.
View example |
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Orthologues between Arabidopsis thaliana and Oryza sativa ssp. japonica were identified using INPARANOID (13-JAN-09)
• Based on the modification of the best bidirectional hit approach, implemented in INPARANOID we have identified orthologues and co-orthologues in Arabidospsis and Rice.
Only genes with a inparalog score greater than 0.7 and a bootstrap value greater than 95% are shown.
View example |
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New download functionalities in GabiPD (09-JAN-09)
• Large datasets and software can now be downloaded from the "Download" page. |
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Partial sequences of 91 BAC clones from Hordeum vulgare cultivar Morex are exclusively available for WPG participants (19-DEC-08)
• Sequences were generated using 454 technology within the GABI-BARLEX project at IPK.
• Please find the data via GreenCards with the keyword "HVVMRXALLhA*". |
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The Oryza sativa ssp. japonica genome annotation (TIGR5) has been integrated in GabiPD (17-DEC-08)
• Conserved protein domains are displayed on the sequence and corresponding barley ESTs are similarity-based mapped.
View example |
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GeneOntology annotation for Arabidopsis thaliana and Oryza sativa ssp. japonica sequences has been integrated in GabiPD (17-DEC-08)
• View example |
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A new release candidate of MapMan desktop is available (03-DEC-08)
• This version (v3.0.0RC1) features the simultaneous visualization of multiple assays as well as lots of enhancements.
Download |
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About 2.800 Sugar beet ESTs from Sugar Beet Seed publicly available (28-OCT-08)
• A related publication is in press in BMC Plant Biology (E. Pestsova et al. 2008).
• Search for the data using GreenCards with the keyword "FG3*". |
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A new version of MapMan desktop is available (15-SEP-08)
• This version (v2.2.0) is able to map gene expression data onto Arabidopsis chromosome maps, and includes a new simplified first-user interface.
Download |
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Sugar beet GSS sequences from GABI BeetSeq publicly available (29-AUG-08)
• These 2.815 GSS (fosmid ends) from the sugar beet DH line KWS2320 were generated in the GABI BeetSeq project. The data have recently been published in Genome
(C. Lange et al. 2008).
• Please find the data via GreenCards searching for "IGS-SCF*". |
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New Gene GreenCard with NCBI UniGene information for all GabiPD sequences (07-AUG-08)
• Based on the best BLAST hit against Uniprot all GabiPD sequences are linked to the new Gene GreenCard with NCBI UniGene information and vice versa.
View an example |
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SATlotyper - a new software tool - available for download (07-AUG-08)
• SATlotyper is designed for inferring haplotypes and phased genotypes from unphased SNP data for polyploid and polyallelic heterozygous populations.
• This tool developed by the GabiPD team has recently been published in BMC Genomics.
(J. Neigenfind et al. 2008).
Download and more information |
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All potato maps updated (25-JUL-08)
• Potato genetic and physical maps as well as Solanaceae Functional Maps were updated.
View and download mapping data. |
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Conserved protein domains displayed on barley ESTs (25-JUL-08)
• Conserved protein domains are displayed on the barley EST sequences in GabiPD.
View an example |
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Arabidopsis Gene GreenCards upgraded (12-JUN-08)
• The cDNA display in the Gene GreenCard is extended by new graphical features:
• Conserved protein domains are displayed on the sequence and corresponding ESTs are similarity-based mapped. Exon-exon borders are visualised.
View an example |
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About 2.800 new Sugar beet EST sequences exclusively available for WPG participants (02-JUN-08)
• Most of the sequences were generated within the GABI-Genoplante joint project Sugar Beet Seed.
• Please find the data via
GreenCards searching for "FG3*". |
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The new Gene GreenCard in GabiPD offers comprehensive gene-specific information for Arabidopsis (02-JUN-08)
• All Arabidopsis data types are pointing now to the central Gene GreenCard.
• With the Gene GreenCard links to genome annotation databases as well as other GABI and external resources are provided: e.g., ARAMEMNON, PhosPhAt and PlnTFDB.
Search for your AGI code of interest
View an example |
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Sugar beet GSS sequences from GABI BeetSeq available (22-MAY-08)
• 2.815 GSS (fosmid ends) from the sugar beet DH line KWS2320 generated in the GABI BeetSeq project were cleaned and submitted to the GenBank by the GabiPD team. Sequences in GabiPD are exclusively available for all WPG-participants.
• Please find the data via
GreenCards searching for "IGS-SCF*". |
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New GabiPD web address (22-APR-08)
• The GabiPD webpage is accessible via a new URL: www.gabipd.org. Nevertheless it is still possible to use the old web address. |
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Potato SNP data is now available (22-APR-08)
• Potato SNP data from 24 different loci generated in the GABI-CONQUEST 2 project are exclusively available for all WPG-participants.
An example |
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Barley clone list representing a new 27K UniGene set is now available (07-FEB-08)
• 459.231 ESTs (from the IPK and public resources) were clustered by the GabiPD team in cooperation with the IPK Gatersleben.
• Based on this assembly a list of IPK cDNA clones enriched for full-length clones was created.
Clone list
More information
Example contig |
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Barley EST sequences from the IPK Gatersleben public (07-FEB-08)
• Over 10.000 RUS-sequences from different cDNA libraries were generated within GABI-SEED.
Please find the data via GreenCards searching for "RUS*". |
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Over 29.000 new barley EST sequences from the IPK Gatersleben public (18-DEC-07)
• These sequences from the HDP library were generated within GABI-PLANT.
Please find the data via
GreenCards searching for "HDP*". |
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All GabiPD sequences blasted against Uniprot_Swissprot (22-NOV-07)
• Please find the Blasthits with the sequences
An example |
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New MapMan version available for download (22-OCT-07)
• Version 2.1.1 from 12.09.2007 includes clustering visualization, many usability enhancements and bug fixes
Download |
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Metabolite data are displayed now via MapManWeb (21-SEP-07)
• Please find sets of metabolite profiling data in combination with gene expression data from Arabidopsis diurnal cycle provided by ARABIDOPSIS-Verbund III.
View metabolite data (Diurnal Cycle) |
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About 29.400 new barley EST sequences from GABI-PLANT (31-JUL-07)
• Data are exclusively accessible for all WPG participants. Find these data via
GreenCards searching for "HDP*". |
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The GabiPD team has moved to the Max Planck Institute for Molecular Plant Physiology Potsdam-Golm (31-JUL-07)
• We will continue the GABI Primary Database Service during GABI-Future based on further funding by the BMBF.
Contact us. |
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Sugar beet genomic RFLP sequences from GABI-BEET are now available (31-JUL-07)
• These data have been published in Theoretical and Applied Genetics. (Schneider K. et al. 2007). Search for these data via GreenCards, combining "Beta vulgaris" with the submitter names "Schneider"or "Jung". |
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Medicago truncatula gene expression data are now available via MapManWeb in GabiPD (31-MAY-07)
• Defense-associated gene expression in Medicago is suppressed by LPS of the microsymbiont Sinorhizobium meliloti
(Tellström, Usadel et al. 2007).
View gene expression data More MapMan information |
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Barley cDNA clones in E. coli expression vector are exclusively available at RZPD (14-FEB-07)
• About 3,900 Barley cDNA clones in the E. coli expression vector pQE30NST from GABI-SEED and GABI-LAPP are now available (Kramer et al. 2004).
Detailed clone information Visit GabiPD's BioMaterials |
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Sugar beet genomic RFLP sequences from GABI-BEET available (14-DEC-06)
• These data are exclusively accessible for all WPG participants. Search for these data via GreenCards, combining "Beta vulgaris" with the submitter names "Schneider"or "Jung". |
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Barley mapping data (14-DEC-06)
• Barley mapping data from the GABI-Map project are now public available. Go to Maps to view mapping data of the seven barley chromosomes or to GreenCards to search for elements mapped on barley chromosomes by keyword. Related EST sequence information is provided with the marker descriptions. |
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Proteomic data from Brassica napus accessible (09-NOV-06)
• Go to Proteomics to view interactive 2D gels from Julia Kehr's group (Max Planck Institute for Molecular Plant Physiology) |
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Potato EST sequences (24-OCT-06)
• More than 6.800 new potato EST sequences from GABI-Genosome are now public available (libraries SSBN, SSBT, STDB, SDBT, SDBN). Search for these data via GreenCards |
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New MapMan version available for download (23-SEP-06)
• MapMan 2.0.0 With filtering support for derived values (p-values..) .
Download |
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New Project BreedCAM (08-AUG-06)
• BreedCAM (Breeding Cultivation and Measurement) provides
access to LfL results of cultivation for different Barley
varieties.
More information |
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Access GabiPD via BioMoby (08-AUG-06)
• Parts of the GabiPD are now available through the BioMoby
WebService.
More information |
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Trace files visualisable through web (08-AUG-06)
• About 20.000 trace files are now integrated into GabiPD and
can be viewed as image and explored via JavaApplet.
Screeshots of traces containing SNPs stored in GabiPD: trace1 , trace2
Full
EST example |
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Arabidopsis expression clones exclusively available from the RZPD (01-JUN-06)
• About 4,500 cDNA clones for expression of His-tagged
proteins are now available from the RZPD (Feilner et al. 2005). These clones are compatible with Gateway recombinational cloning by attB-sites.
More information UNIgene clone set |
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Frame prediction provided for Arabidopsis expression clones (01-JUN-06)
• For about 4,400 of the expression clones, frame prediction is provided within the clone description.
For example |
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More than 18,000 Arabidopsis cDNA / full ORF clones available from the RZPD (01-JUN-06)
• Sequence information, ORF prediction, and Blast results provided for all of these clones. Search for your clone of interest using AGI code, Genebank accession, clone ID, or sequence name in GreenCards.
Search for all clones More information |
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New MapMan version available for download (30-JAN-06)
• MapMan 1.8.0 with new graphical symbol visualization to explicitly differentiate between different data types available for download.
Download |
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Bioinformatic Tools for sequence analysis (14-DEC-05)
• Some bioinformatic tools for sequence analysis are accessible via GabiPD. The tools are from the EMBOSS package. To use this tools, go to GabiPD Biotools |
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Barley EST sequences (13-DEC-05)
• More than 10.000 new barley EST sequences available. These data are exclusively accessible for all WPG and GABI participants. Search for these data via GreenCards |
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Potato EST sequences (13-DEC-05)
• More than 6.000 new potato EST sequences from GABI-Genosome available. These data are exclusively accessible for all WPG and GABI participants. Search for these data via GreenCards |
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Potato mapping data available for download (04-NOV-05)
• Download of genetic maps of potato chromosomes I to XII.
Download |
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New MapMan version available for download (21-SEP-05)
• MapMan version 1.6.3 available for download. News: statistics, advanced data loading, legend and linkout.
Download |
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Solanaceae function maps for pathogen resistance (21-SEP-05)
• The 'SOLanaceae Function Map for Pathogen Resistance' has been compiled by Christiane Gebhardt (MPI for Plant Breeding Research, Köln, Germany, gebhardt@mpiz-koeln.mpg.de).
View maps |
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Full ORF Arabidopsis clones available (30-AUG-05)
• About 1000 Arabidopsis full ORF clones available from RZPD.
More information |
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Arabidopsis expression clones (15-AUG-05)
• Sequence information on about 4,600 Arabidopsis cDNA expression clones are accessible. All clones will be available from RZPD shortly.
More information |
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Arabidopsis T-DNA lines (18-APR-05)
• Version 17 of GABI-KATs Arabidopsis T-DNA lines available. Search for this data via GreenCards |
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Arabidopsis gene expression data (04-JAN-05)
• View Arabidopsis gene expression from AtGenExpress via MapManWeb. View data. |
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Brassica napus EST sequences (14-DEC-04)
• More than 8.500 EST sequences from Brassica napus accessible. Search for this data via GreenCards. |
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More than 19.000 new EST sequences from barley (06-OCT-04)
• These GABI-AGROTEC data are exclusively accessible for all WPG and GABI participants. Search for these data via GreenCards. |
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Barley mapping data (16-JUL-04)
• Barley mapping data from the GABI-Map project are exclusively accessible for all WPG partners. Go to Maps to view mapping data of the seven barley chromosomes or to GreenCards to search for elements mapped on barley chromosomes by keyword. |
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Barley BAC sequence (07-JUL-04)
• BAC contig_rym4: 439 kb of barley chromosome 3HL, region around rym4 gene exclusively accessible for WPG partners.
Login and view BAC-sequence via GreenCards. |
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Download Arabidopsis 2D-gel images and data (29-JAN-04)
• Overview and download of 2D-gels of different tissues (inflorescence, stem, primary leaf, leaf, seed, seedling, silique, root). |
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Download MapMan (28-JAN-04)
• MapMan is a user-driven tool that displays large datasets (e.g. gene expression data from Arabidopsis Affymetrix arrays) onto diagrams of metabolic pathways or other processes. |
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More than 7.000 new EST sequences from barley (27-JAN-04)
• These GABI-AGROTEC data are exclusively accessible for all WPG and GABI participants. Search for these data via GreenCards. |
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Barley cDNA clones (28-NOV-03)
• Sequence information on more than 3900 Barley cDNA clones (cloned in expression vector) are exclusively accessible for all WPG participants. Login and go to GreenCards to get access to these data. |
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Arabidopsis Proteomics data accessible (13-NOV-03)
• Proteomics data from the GABI-LAPP project are accessible. Go to Proteomics to view interactive 2D gels.
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Arabidopsis cDNA clones (13-NOV-03)
• Sequence information on more than 4500 Arabidopsis cDNA clones (cloned in expression vector) are exclusively accessible for all WPG participants. Login and go to GreenCards to get access to these data. |
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Maps of all twelve potato chromosomes (30-SEP-03)
• Data are exclusively accessible for all GABI and WPG participants. Go to Maps to view mapping data. |
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16.000 new EST sequences from barley (18-SEP-03)
• Data are exclusively accessible for all WPG participants. Search for these data via GreenCards. |
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Potato SNPs and InDels (17-SEP-03)
• SNP and InDel data from diverse di- and tetraploid potato strains are accessible via GabiPD. Data are from the GABI-CONQUEST project. Search for these data via GreenCards. |
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Download (16-SEP-03)
• Download: Arabidopsis genes (annotated by AGI or CATMA) represented on Affymetrix chip. |
