iConvert

iConvert standardizes and consolidates SNP array data across major livestock species to enable interoperable annotation and integration with genome assemblies and public databases such as Ensembl.

Key Features:

• Data integration and standardization: Consolidates array-specific information including SNP IDs and allele coding and aligns species-specific details such as past and current genome assemblies for cows, pigs, horses, sheep, goats, and chickens.
• MySQL database backend: Stores integrated SNP and array metadata in a MySQL database populated with original data sourced from SNP array producers and international genome consortia.
• Interoperability with public databases: Maps array-producer information to public resources such as Ensembl to enable direct cross-referencing and annotation without requiring additional pipelines.
• Multi-array and multi-species support: Handles variable numbers of SNP arrays across species (e.g., one for goats to over ten for cattle) to facilitate comparative analyses.
• Ensembl E!mpowered integration: Uses Ensembl resources as an Ensembl E!mpowered tool to align array information with Ensembl annotations.

Scientific Applications:

• Genetic improvement: Provides standardized SNP data to support selection and breeding strategies for trait enhancement in livestock.
• Association studies: Enables identification and annotation of genetic markers linked to phenotypes or diseases.
• Cross-species comparative genomics: Facilitates comparative genomic analyses across different livestock species to investigate evolutionary relationships and functional genomics.

Methodology:

Collects data from SNP array producers and international genome consortia, integrates SNP IDs, allele coding, and genome assembly mappings, and stores the consolidated metadata in a MySQL database.