This page provides an overview over the various tools developed by PGSB to query, explore and analyse plant genome data in the framework of PlantsDB.
transPLANT is a consortium of 11 European partners
gathered to address these challenges and to develop a
trans-national infrastructure for plant genomic science.
Bringing together groups with strengths in data analysis,
plant science, computer science, and from the academic and
commercial sectors, transPLANT will develop integrated
standards and services and undertake new research and
development needed to capitalise on the sequencing
revolution, across the spectrum of agricultural and model
CrowsNest is a Comparative Map Viewer at PGSB that uses a
dynamic graphical interface to visualize and investigate
genome-wide chromsome organization as well as genome-wide
synteny between two or more plant genomes.
Drought is one of the major constraints of plant productivity world wide.
To cope with reduced water availability, plants exhibit a number of physiological
and molecular drought avoidance and drought tolerance mechanisms.
Genes involved in drought response can contribute directly to increased stress tolerance
by for example encoding protection factors or enzymes for osmolyte biosynthesis.
This database integrates a number of drought stress genes manually extracted and curated from
relevant literature and links them with their genomic resources and orthologs in other species.
The RNASeqExpressionBrowser is a web-based tool which
provides means for search and visualization of RNA-seq
expression data (e.g. based on sequence-information or
domain annotations). It can generate detailed reports for
selected genes including expression data and associated
chromoWIZ is a user-friendly web tool that allows
visualizing the genomic positions of relevant genes and
allows comparing these data between different plant
The repeateElement database PGSB-REdat version9.0p
contains currently around 42.000 sequences, with a focus
on de novo detected LTR-retrotransposons from grass
(~28.000) and other (~9.000) genomes hosted in PlantsDB.
The repeat elements are classified by PGSB-REcat, a
hierarchical repeats classification catalog, which
facilitates data extraction at different levels of detail.