Crop Analysis Tool Suite (CATS)

Crop Analysis Tool Suite (CATS) provides integrated bioinformatics analyses for Triticeae genomics, including homology search, repeat masking, microsatellite detection, genebank-scale data integration, and genome visualization for barley (Hordeum vulgare), rye, and bread wheat.

Key Features:

• BLAST Server: Performs homology searches against cereal genome resources to identify sequence similarities within barley, rye, and bread wheat genomes.
• Kmasker Plants: Conducts in silico masking of repetitive sequences from ten agronomically important plants and extracts unique genomic sequences suitable for fluorescence in situ hybridization (FISH) and guideRNA construction for CRISPR applications.
• MISA Web: Detects microsatellites including compound microsatellites from resequencing data and supports result export in GFF3 format.
• BRIDGE: Serves as a genebank genomics data warehouse integrating genotypic and phenotypic data from 22,626 barley accessions with interactive visualization of sequence polymorphisms, phenotyped traits, and geographic distribution plus modules for dimensionality reduction and genome-wide association studies (GWAS) and export to VCF and ISA-Tab.
• Barley Genome Explorer (BARLEX): Provides reference genome visualization for barley enriched with expression data, repeat annotations, gene annotations, and molecular marker data.

Scientific Applications:

• Genome-Scale Research: Integrating and exchanging complex Triticeae genome data across distributed resources for large-genome analyses.
• Breeding and Conservation: Enabling use of plant genetic resources to develop stress-resistant cultivars and preserve genetic diversity.
• Comparative Genomics: Facilitating comparative analysis of Triticeae genomes to study genome organization and evolution.
• Genotype-Phenotype Linkage: Connecting genotypic data with phenotypic traits to support functional genomics and trait mapping.

Methodology:

Computational methods explicitly include BLAST homology searches; in silico repeat masking and unique-sequence extraction with Kmasker; microsatellite detection including compound microsatellites with MISA Web and GFF3 export; integration of genotypic and phenotypic data from 22,626 barley accessions in the BRIDGE data warehouse; exploratory analyses including dimensionality reduction and GWAS; data export in VCF and ISA-Tab; and genome visualization combining expression data, repeat annotations, gene annotations, molecular marker data, sequence polymorphisms, phenotypes, and geographic distribution.