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An interactive bovine in silico SNP database (IBISS)

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Abstract

An interactive bovine in silico SNP (IBISS) database has been created through the clustering and aligning of bovine EST and mRNA sequences. Approximately 324,000 EST and mRNA sequences were clustered to produce 29,965 clusters (producing 48,679 consensus sequences) and 48,565 singletons. A SNP screening regime was placed on variations detected in the multiple sequence alignment files to determine which SNPs are more likely to be real rather than sequencing errors. A small subset of predicted SNPs was validated on a diverse set of bovine DNA samples using PCR amplification and sequencing. Fifty percent of the predicted SNPs in the “putative >1” category were polymorphic in the population sampled. The IBISS database represents more than just a SNP database; it is also a genomic database containing uniformly annotated predicted gene mRNA and protein sequences, gene structure, and genomic organization information.

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Acknowledgments

The authors would like to thank the entire Bioinformatics team at CSIRO LI and the staff at Electric Genetics for their assistance in using StackPACK to cluster these sequences. The authors also thank Bill Barendse and James Kijas for helpful and insightful discussions regarding specific areas of this paper. We thank Bill Barendse for cattle DNA samples and access to an ABI 377 DNA sequencer.

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Authors and Affiliations

  1. Queensland Bioscience Precinct, CSIRO Livestock Industries, 306 Carmody Road, St. Lucia, Australia

    Rachel J. Hawken, Wesley C. Barris, Sean M. McWilliam & Brian P. Dalrymple

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  1. Rachel J. Hawken
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  2. Wesley C. Barris
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  3. Sean M. McWilliam
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  4. Brian P. Dalrymple
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Correspondence to Rachel J. Hawken.

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Hawken, R.J., Barris, W.C., McWilliam, S. et al. An interactive bovine in silico SNP database (IBISS). Mamm Genome 15, 819–827 (2004). https://doi.org/10.1007/s00335-004-2382-4

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