PlabiPD - Providing Crop Data for Plant Research

There are many challenges facing the scientific community when dealing with Big Data. PlabiPD is a resource which focuses on tackling these challenges by presenting Big Data to the users in an intuitive and user friendly manner. We have currently integrated crop genome data together with manually curated data into PlabiPD which is hosted at the research center Jülich, Germany.

We have used our experience in developing next generation pipeline tools, such as Trimmomatic and MapMan, to devise novel ways to analyse, visualize and present large datasets. We have taken the protein data from multiple plant species and clustered these data using the Markov Cluster Algorithm. Subsequently, manually curated data from Arabidopsis stemming from the Aramemnon database as well as from model and crop plants originating from the MapMan project was used to annotate the clustered proteins. Users are thus able to find orthologous proteins in the other crop plants based on high quality manual annotations. Additional information such as protein coding regions along with conserved domains (Pfam) are also presented in a user friendly interface. Links from individual genes provide direct access to extended information hosted on the species-specific websites. We additionally provide graphical timeline visualizations for every new published plant genome.

Back to: Bioinformatics: Databases

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