Helmholtz Zentrum München - German Research Center for Environmental Health

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.

The TransPLANT Genome Resources Registry

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 plant species.
[LINK]


CrowsNest - Comparative Map Viewer

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.
[LINK]


ExpressionBrowser

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 annotations.
[LINK]


chromoWIZ

chromoWIZ is a user-friendly web tool that allows visualizing the genomic positions of relevant genes and allows comparing these data between different plant genomes.
[LINK].


PGSB Repeat Element database (PGSB-REdat)
PGSB Repeat Element catalog (PGSB-REcat)

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.
[LINK]