Crop Analysis Tools Suite (CATS)
The several software tools for sequence analysis, especially of plants, are provided by the IPK Gatersleben as a tool suite:
- The web BLAST server based on Galaxy utilizes a homology search against current crop (pan-) genome sequence resources.
- MISA web searches a nucleotide sequence for microsatellites and is able generate molecular markers or primers.
- PanBARLEX is a comprehensive web portal providing access to gene annotations and orthologous gene groups for 76 barley genotypes, featuring 3.8 million annotated genes and versatile tools for gene searches, including BLAST, visualization and analysis to support barley pan-genome research.
- The barley genome explorer (BARLEX) is a system to visually inspect the reference genome sequence of barley, enriched with expression data, repeat and gene annotation as well as molecular marker data.
- Within BRIDGE the complete barley collection of the IPK genebank can be visually explored in an interactive manner through diversity, certain phenotyped traits, and based on sequence polymorphisms.
- Kmasker plants is able to mask sequences originating from ten agronomically important plants based on mathematical defined repeats, furthermore, selection of sequences applicable for guideRNA construction for genome editing (CRISPR) or for fluorescence in situ hybridization is also possible.
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Funding: Development and maintenance partially funded by de.NBI