SNPchiMp v.3: integrating and standardizing single nucleotide polymorphism data for livestock species

Area of Science:

• Livestock genomics
• Bioinformatics
• Animal breeding

Background:

• Genomic information is crucial for livestock genetic improvement and association studies.
• Numerous single nucleotide polymorphism (SNP) arrays exist for livestock, varying in content and density.
• Lack of standardization and integration for array-specific and species-specific SNP data hinders usability.

Purpose of the Study:

• To present SNPchiMp v.3, a solution for standardizing and integrating SNP array data.
• To address the challenges of diverse SNP array content and species-specific information.
• To provide a user-friendly platform for livestock genomic data management.

Main Methods:

• Collected original data from SNP array producers and genome consortia.
• Stored data in a MySQL database.
• Developed an open-access web tool linking the database to public resources.

Main Results:

• SNPchiMp v.3 provides standardized and integrated genomic data for cattle, pigs, horses, sheep, goats, and chickens.
• The platform ensures fast retrieval of within/across SNP array data.
• SNPchiMp v.3 enables user-friendly annotation of SNP array data.

Conclusions:

• SNPchiMp v.3 facilitates easy integration and standardization of livestock genomic data for research and industry.
• Users can seamlessly link array producer information with public database data.
• The tool is recognized as an Ensembl E!mpowered tool, highlighting its value and integration with public resources.