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An interactive bovine in silico SNP database (IBISS).

Rachel J Hawken1, Wesley C Barris, Sean M McWilliam

  • 1Queensland Bioscience Precinct, CSIRO Livestock Industries, 306 Carmody Road, St. Lucia, Australia. rachel.hawken@csiro.au.

Mammalian Genome : Official Journal of the International Mammalian Genome Society
|November 3, 2004
PubMed
Summary

A new bovine in silico SNP (IBISS) database was developed using extensive sequence data. This genomic resource identifies and validates single nucleotide polymorphisms (SNPs) for cattle genetic research.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Molecular Biology

Background:

  • Development of comprehensive genomic resources is crucial for cattle genetic improvement.
  • Identifying single nucleotide polymorphisms (SNPs) aids in understanding genetic variation and trait association.

Purpose of the Study:

  • To create an interactive bovine in silico SNP (IBISS) database.
  • To identify and validate SNPs from bovine expressed sequence tags (ESTs) and mRNA sequences.
  • To provide a valuable genomic resource for cattle research.

Main Methods:

  • Clustering and aligning approximately 324,000 bovine EST and mRNA sequences.
  • Implementing a SNP screening regime on multiple sequence alignments to filter real variations.
  • Validating predicted SNPs using PCR amplification and sequencing on diverse bovine DNA samples.

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Main Results:

  • Generated 29,965 clusters and 48,565 singletons from sequence data.
  • Identified a subset of SNPs, with 50% validation rate in the 'putative >1' category.
  • The IBISS database contains annotated gene sequences, structures, and genomic organization.

Conclusions:

  • The IBISS database is a significant genomic resource for bovine research.
  • It facilitates the discovery and utilization of SNPs in cattle.
  • The database integrates SNP information with gene and genomic organization data.