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PlabiPD database

The current implementation of the PlaBi dataBase focuses on seven crop plants which includes sugar beet, grapevine, rapeseed (canola), potato, maize, barley and bread wheat. The model plant Arabidopsis thaliana is also included as this model plant is used as a reference.

Sequence data
For all protein-coding genes of the seven crop plants and the one model plant the protein sequence, the cDNA sequence and the genomic sequence (including ~1800 bp of the 5'-UTR and ~300 bp of the 3'-UTR) is available. In addition, conserved protein domains as specified by the PFAM 31.0 database are shown.

Genome browser
The portal provides a JBrowser genome browser implementation for several of these plants which allows visualization of genetic data from chromosome to gene level.

Protein family data
The protein data from the seven crop plants and one model plant have been clustered using the Markov Cluster Algorithm (MCL). This data is then used in the database to allow the users to find orthologous proteins in the eight plants currently available.

Funding

This project Pflanzen-Primärdatenbank PPD was funded by the Federal Ministry of Education and Research (BMBF). The BMBF also funded the prior project GABI Primärdatenbank.

    Funding history including Förderkennzeichen (FKZ)
  • 01.01.2000 until 30.04.2004 FKZ: 0312272/6 (GABI-Primärdatenbank)
  • 01.05.2004 until 31.07.2007 FKZ: 0313112 (GABI-Primärdatenbank)
  • 01.08.2007 until 31.12.2012 FKZ: 0315046 (GABI-Primärdatenbank)
  • 01.05.2013 until 31.12.2016 FKZ: 0315961 (Pflanzen-Primärdatenbank PPD)

search by protein

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search by nucleotide sequence

Hordeum vulgare

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include 5'/3'-UTRs


Triticum aestivum

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include 5'/3'-UTRs

Zea mays

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include 5'/3'-UTRs


Brassica napus

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include 5'/3'-UTRs




Solanum tuberosum

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include 5'/3'-UTRs


Beta vulgaris

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include 5'/3'-UTRs

Vitis vinifera

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include 5'/3'-UTRs


Arabidopsis thaliana

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include 5'/3'-UTRs


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