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Mining for SNPs and SSRs using SNPServer, dbSNP and SSR taxonomy tree
Jacqueline Batley1, David Edwards
1Australian Centre for Plant Functional Genomics, School of Land, Crop and Food Sciences, University of Queensland, Brisbane, Australia.
Methods in Molecular Biology (Clifton, N.J.)
|April 21, 2009
Summary
Automated web tools discover molecular genetic markers, including single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs), aiding genetic trait mapping and agricultural applications.
Area of Science:
- Genetics and Genomics
- Bioinformatics
- Molecular Biology
Background:
- Molecular genetic markers are crucial for genome analysis and associating traits with genetic variation.
- High-throughput methods for single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) have advanced their utility.
- Large sequence datasets enable mining for molecular markers used in agriculture and research.
Purpose of the Study:
- To describe web-based automated methods for discovering molecular genetic markers.
- To facilitate the identification of SSRs and SNPs for various genetic applications.
Main Methods:
- Utilized SSR taxonomy tree for pre-determined SSR amplification primer discovery across species in GenBank.
- Employed SNPServer for SNP discovery from DNA sequences using BLAST, CAP3, and autoSNP.
- Integrated data from the NCBI dbSNP database for validated SNP identification.
Main Results:
- SSR taxonomy tree provides SSR primers for numerous species.
- SNPServer effectively identifies SNPs and insertion/deletion polymorphisms from sequence data.
- dbSNP database serves as a public archive for validated SNPs.
Conclusions:
- Developed efficient, automated web tools for discovering SSRs and SNPs.
- These tools enhance the application of molecular markers in genetic research and agriculture.
- Facilitated access to validated SNP data through integration with public databases.
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