GABIinfo - The Bioinformatic Information Resorce for the GABI network
GABI is an associative project supported by the German federal ministry for education, research and technology (BMBF) as well as by business companies. These companies are comprised in the economic association for biotechnology GABI e.V. (WPG). GABI was started at the end of 1999. In a first step, 63 single projects with a total financial volume of about Euro 40 million are supported.
GABI's objectives are to strengthen the German plant genome research on the international level, to create a national network and to establishe of competence centres. Additional goals are the gain of information on the structures and functions of important plant genomes, technology transfer between research institutes and business companies, patenting and thereby hence disclosure of research results and improvement of the international cooperation.
GABIinfos aim is to develop bioinformatics resources for plant genome data and to provide w3 accessible information. This objective comprises maintainance of existing resources, development of bioinformatic tools and applications as well as structuring, analysing and integrating the drastically increasing amount of heterogeneous data publicly available from a wide range of different plant species. A further goal of GABIinfo is the collaboration and interaction with experimental groups within GABI and to integrate GABI generated data on a genomewide scale with to enable the complex analysis on heterogenous datasets and to summarize the analysis results in adequate comprehensible representations.
Individual components of our efforts are:
The MIPS Arabidopsis thaliana Database MAtDB
Arabidopsis thaliana is the first plant for which the complete genome has been sequenced. In order to put the wealth of information represented by the
complete genome sequence to use, we must learn to decode this information and to connect it to diverse biological data. A list of all genes of an organism is
no more than a list of parts; we need to discover their functions and interactions in order to understand the workings of the whole. The MIPS Arabidopsis
thaliana database (MAtDB) started out as a repository for genome
sequence data in the European Scientists Sequencing Arabidopsis (ESSA) project, part of the Arabidopsis Genome Initiative, but is moving towards
becoming an integrated biological knowledge resource by integrating diverse data, tools, query and visualization capabilities. The aim is to create a
comprehensive resource for Arabidopsis as a model that can then be used to transfer knowledge onto sequences from other species, including crop plants.
A new version of MAtDB includes TIGR annotation and MAtDB annotation in a new look and feel, try it here.
The MIPS Oryza sativa Database MOsDB
Although of wide use as a model system for plants in general, Arabidopsis has limitations to serve as a model for monocotelydoneous plants and genomes.
Thus the efforts undertaken in public consortia to sequence and analyse the rice genome are of high importance as a genome reference system for
monocotelydoneous research. Recently the complete sequencing of the rice genome (spp. indica) was published and large amounts of rice spp. japonica
have been made accessible to the public. The MIPS rice database MOsDB aims to structure and analyse the data in a similar standard as the Arabidopsis
genome data. The functionality will include various searchability options, functional categorisation, transparent gene assignment,among others, and will allow
to carry out in silicio comparative genomics.
The MIPS Oryza sativa Database (MOsDB) is a resource for publicly available sequences of the rice (Oryza sativa L.) genome. MOsDB is back online in a
completely new look and feel.
The MIPS Medicago truncatula Database URMeLDB
In contrast to Arabidopsis and other plants, Medicago truncatula has the ability to fix atmospheric nitrogen and therefore serves as a model
organism for the legumes plant family. In addition, legumes have the capacity to establish the formation of endomycorrhizae, a root endosymbiosis important
with plant mineral nutrition. As a consequence, legumes have developed the ability to accumulate remarkable levels of proteins.
To reveal the genetic programme for symbiotic nitrogen fixation and due to its resulting relevance for both biology and agriculture, Medicago truncatula's
genome is sequenced and annotated within an international consortium. Within the participation of the European Grain Legume Project (funded by the European
Union) the MIPS Medicago Database aims to collect, structure, analyse and present the data produced within the project in a comprehensive manner. The
functionality will include various searchability options, functional categorisation, visual genome browsing and will allow in silicio comparative genomics.
The MIPS Medicago truncatula Database (URMeLDB) is a resource for publicly available sequences of the Medicago truncatula genome.
SPUTNIK-Exhaustive and comprehensive Analysis of Plant derived EST sequences
While no or only restriced large-scale genomic sequences may become available for these species in the near future, there is a large short cut to access partial transcriptomic sequences. ESTs have been a popular target for sequencing within the recent years and in total there are in excess of 1.8 million plant-derived ESTs within the public domain. While ESTs are beset with issues of redundancy, questionable quality and short read-length, they are a solid and computable form of data that stems directly from the plant transcriptome.
Sputnik has been implemented as a largely automated pipeline for the processing, clustering and annotation of large numbers of EST sequences. From the non-redundant cluster set, peptide sequences can be derived - and with this, large scale genomic analyses can be performed with the partial reconstructed proteome. "Genomeless genomics" has been termed to describe the application of complete-genomic analyses to such reconstructed genomes.
Bioinformatic Detection of regulatory Elements in Plants
It is of vital importance for every organism to tightly regulate the activity of its genes temporally and/or spatially in response to various external and internal stimuli. The specific expression of each gene results from specific cis-regulatory elements in non-coding regions, especially the 5' upstream region. Our projects will detect new candidates of cis-regulatory elements in plant genomes by combining several approaches (phylogenetic footprinting, enumerative methods). These motifs will be evaluated by statistical validation and by comparing our results to known cis-regulatory sites in plants.
PLANET - a Network of European Plant databases
PlaNet aims to develop and deliver a high level plant genome database for the systematic exploration of Arabidopsis and other plants. The completion of Arabidopsis' 120 million base pair genome in late 2000 marked a milestone in genome based biology. A network of European scientists significantly contributed to this success by completing chromosomes III, IV and V. In addition to the sequencing efforts, about half of the genome has been annotated at the IBI. Functional genomics efforts to eludicate the functional role of each individual gene in Arabidopsis as well as the analysis of genes in crop species are subject of national networks in europe, namely the GABI, GarNet and Genoplante networks.
The information on plant genes is of the upmost importance for the future development of agricultural and environmental research. Since the information resulting from experiments and bioinformatic interpretation is highly complex, the compilation of information resources requires dynamic information acquisition, expert curation and the integration of bioinformatics methods. PlaNet is a distributed, europeanwide shared effort among both experienced bioinformatics groups and plant molecular biologists to establish a comprehensive integrated database in a collaborative network.
PLASMAR - plant comparative genome analysis
The aim of the proposed work is to study plant small RNAs through the development of advanced genomic tools. The present state of knowledge on the functions of endogenous small RNAs in plants is limited, and many questions remain unresolved, in particular the possible implication of these molecules on gene regulation in response to abiotic and biotic stress conditions. Our integrated strategy will use both experimental and bioinformatic approaches to address search for candidate genes that are possibly regulated by small RNAs, and in the development of computer-based algorithms for prediction of small RNA precursors as well as stress-responsive elements in their promoters. Following experimental validation of the most relevant results, we propose the generation of a micro-array containing plant small RNAs that will be used to extend our study to different plant species. Comparative genomics approaches will give broad biodiversity dimension to the work through the identification of conserved stress-related small RNAs and possible specific adaptations to stress by diversification.
