Skip to main content
SpringerLink
Log in

Mining for SNPs and SSRs Using SNPServer, dbSNP and SSR Taxonomy Tree

  • Protocol
  • First Online:
Bioinformatics for DNA Sequence Analysis

Part of the book series: Methods in Molecular Biology ((MIMB,volume 537))

Abstract

Molecular genetic markers represent one of the most powerful tools for the analysis of genomes and the association of heritable traits with underlying genetic variation. The development of high-throughput methods for the detection of single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) has led to a revolution in their use as molecular markers. The availability of large sequence data sets permits mining for these molecular markers, which may then be used for applications such as genetic trait mapping, diversity analysis and marker assisted selection in agriculture. Here we describe web-based automated methods for the discovery of SSRs using SSR taxonomy tree, the discovery of SNPs from sequence data using SNPServer and the identification of validated SNPs from within the dbSNP database. SSR taxonomy tree identifies pre-determined SSR amplification primers for virtually all species represented within the GenBank database. SNPServer uses a redundancy based approach to identify SNPs within DNA sequences. Following submission of a sequence of interest, SNPServer uses BLAST to identify similar sequences, CAP3 to cluster and assemble these sequences and then the SNP discovery software autoSNP to detect SNPs and insertion/deletion (indel) polymorphisms. The NCBI dbSNP database is a catalogue of molecular variation, hosting validated SNPs for several species within a public-domain archive.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Brumfield, R. T., Beerli, P., Nickerson, D. A., and Edwards, S. V. (2003) The utility of single nucleotide polymorphisms in inferences of population history. Trends Ecol Evol 18, 249–56.

    Article  Google Scholar 

  2. Collins, A., Lau, W., and De la Vega, F. M. (2004) Mapping genes for common diseases: The case for genetic (LD) maps. Hum Hered 58, 2–9.

    Article  PubMed  Google Scholar 

  3. Rafalski, A. (2002) Applications of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol 5, 94–100.

    Article  PubMed  CAS  Google Scholar 

  4. Gupta, P. K., Roy, J. K., and Prasad, M. (2001) Single nucleotide polymorphisms: a new paradigm for molecular marker technology and DNA polymorphism detection with emphasis on their use in plants. Curr Sci 80, 524–35.

    CAS  Google Scholar 

  5. Clifford, R., Edmonson, M., Hu, Y., Nguyen, C., Scherpbier, T., and Buetow, K. H. (2000) Expression-based genetic/physical maps of single nucleotide polymorphisms identified by the cancer genome anatomy project. Genome Res 10, 1259–65.

    Article  PubMed  CAS  Google Scholar 

  6. Deutsch, S., Iseli, C., Bucher, P., Antonarakis, S. E., and Scott H. S. (2001) A cSNP map and database for human chromosome 21. Genome Res 11, 300–7.

    PubMed  CAS  Google Scholar 

  7. Edwards, D., Forster, J. W., Chagné, D., and Batley, J. (2007) What are SNPs? in Association Mapping in Plants (Oraguzie N. C., Rikkerink E. H. A, Gardiner S. E. and De Silva H. N., Eds.), Springer New York, pp 41–52.

    Google Scholar 

  8. Syvanen, A. C. (2001) Genotyping single nucleotide polymorphisms. Nat Rev Genet 2, 930–42.

    Article  PubMed  CAS  Google Scholar 

  9. The International HapMap Consortium. (2003) The international HapMap project. Nature 426, 789–96.

    Article  Google Scholar 

  10. Buetow, K. H., Edmonson, M. N., and Cassidy, A. B. (1999) Reliable identification of large numbers of candidate SNPs from public EST data. Nature Genet 21, 323–5.

    Article  PubMed  CAS  Google Scholar 

  11. Gu, Z., Hillier, L., and Kwok, P.-Y. (1998) Single nucleotide polymorphism hunting in cyberspace. Hum Mutat 12, 221–5.

    Article  PubMed  CAS  Google Scholar 

  12. Picoult-Newberg, L., Ideker, T. E., Pohl, M. G., Taylor, S. L., Donaldson, M. A., Nickerson, D. A., and Boyce-Jacino M. (1999) Mining SNPs from EST databases. Genome Res 9, 167–74.

    PubMed  CAS  Google Scholar 

  13. Taillon-Miller, P., Gu, Z., Li, Q., Hillier, L., and Kwok, P.-Y. (1998) Overlapping genomic sequences: a treasure trove of single-nucleotide polymorphisms. Genome Res 8, 748–754.

    PubMed  CAS  Google Scholar 

  14. Adams, M. D., Kerlavage, A. R., Fleischmann, R. D., Fuldner, R. A., Bult, C. J., Lee, N. H., Kirkness, E. F., Weinstock, K. G., Gocayne, J. D., White, O., Sutton, G., Blake, J. A., Brandon, R. G., Chiu, M. W., Clayton, R. A., Cline, R. T., Cotton, M. D., Earlehughes, J., Fine, L. D., Fitzgerald, L. M., Fitzhugh, W. M., Fritchman, J. L., Geoghagen, N. S. M., Glodek, A., Gnehm, C. L., Hanna, M. C., Hedblom, E., Hinkle, P. S., Kelley, J. M., Klimek, K. M., Kelley, J. C., Liu, L. I., Marmaros, S. M., Merrick, J. M., Morenopalanques, R. F., Mcdonald, L. A., Nguyen, D. T., Pellegrino, S. M., Phillips, C. A., Ryder, S. E., Scott, J. L., Saudek, D. M., Shirley, R., Small, K. V., Spriggs, T. A., Utterback, T. R., Weldman, J. F., Li, Y., Barthlow, R., Bednarik, D. P., Cao, L. A., Cepeda, M. A., Coleman, T. A., Collins, E. J., Dimke, D., Feng, P., Ferrie, A., Fischer, C., Hastings, G. A., He, W. W., Hu, J. S., Huddleston, K. A., Greene, J. M., Gruber, J., Hudson, P., Kim, A., Kozak, D. L., Kunsch, C., Ji, H. J., Li, H. D., Meissner, P. S., Olsen, H., Raymond, L., Wei, Y. F., Wing, J., Xu, C., Yu, G. L., Ruben, S. M., Dillon, P. J., Fannon, M. R., Rosen, C. A., Haseltine, W. A., Fields, C., Fraser, C. M., and Venter, J. C. (1995) Initial assessment of human gene diversity and expression patterns based upon 83-million nucleotides of cDNA sequence. Nature 377, (Suppl.) 3–17.

    PubMed  CAS  Google Scholar 

  15. Dawson, E., Chen, Y., Hunt, S., Smink, L. J., Hunt, A., Rice, K., Livingston, S., Bumpstead, S., Bruskiewich, R., Sham, P., Ganske, R., Adams, M., Kawasaki, K., Shimizu, N., Minoshima, S., Roe, B., Bentley, D., and Dunham, I. (2001) A SNP resource for human chromosome 22: extracting dense clusters of SNPs from the genomic sequence. Genome Res 11, 170–8.

    Article  PubMed  CAS  Google Scholar 

  16. Ewing, B., and Green, P. (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8, 186–94.

    PubMed  CAS  Google Scholar 

  17. Ewing, B., Hillier, L., Wendl, M. C., and Green, P. (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8, 175–85.

    PubMed  CAS  Google Scholar 

  18. Batley, J., Barker, G., O’Sullivan, H., Edwards, K. J., and Edwards, D. (2003) Mining for single nucleotide polymorphisms and insertions/deletions in maize expressed sequence tag data. Plant Physiol 132, 84–91.

    Article  PubMed  CAS  Google Scholar 

  19. Barker, G., Batley, J., O’Sullivan, H., Edwards, K. J., and Edwards, D. (2003) Redundancy based detection of sequence polymorphisms in expressed sequence tag data using autoSNP. Bioinformatics 19, 421–2.

    Article  PubMed  CAS  Google Scholar 

  20. Savage, D., Batley, J., Erwin, T., Logan, E., Love, C. G., Lim, G. A. C., Mongin, E., Barker, G., Spangenberg, G.C., and Edwards, D. (2005) SNPServer: a real-time SNP discovery tool. Nucleic Acids Res 33, W493–5.

    Article  PubMed  CAS  Google Scholar 

  21. Huang, X. and Madan, A. (1999) CAP3: a DNA sequence assembly program. Genome Res 9, 868–77.

    Article  PubMed  CAS  Google Scholar 

  22. Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990) Basic local alignment search tool. J Mol Biol 215, 403–10.

    PubMed  CAS  Google Scholar 

  23. Sherry, S. T., Ward, M., and Sirotkin, K. (1999) dbSNP-Database for single nucleotide polymorphisms and other classes of minor genetic variation. Genome Res 9, 677–9.

    PubMed  CAS  Google Scholar 

  24. Smigielski, E. M., Sirotkin, K., Ward, M., and Sherry, S. T. (2000) dbSNP: a database of single nucleotide polymorphisms. Nucleic Acids Res 28, 352–5.

    Article  PubMed  CAS  Google Scholar 

  25. Tóth, G., Gáspári, Z., and Jurka, J. (2000) Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res 10, 967–81.

    Article  PubMed  Google Scholar 

  26. Mortimer, J., Batley, J., Love, C., Logan, E., and Edwards, D. (2005) Simple sequence repeat (SSR) and GC distribution in the Arabidopsis thaliana genome. J Plant Biotechnol 7, 17–25.

    Google Scholar 

  27. Katti, M. V., Ranjekar, P. K., and Gupta, V. S. (2001) Differential distribution of simple sequence repeats in eukaryotic genome sequences. Mol Biol Evol 18, 1161–7.

    Article  PubMed  CAS  Google Scholar 

  28. Schlötterer, C. (2000) Evolutionary dynamics of microsatellite DNA. Nucleic Acids Res 20, 211–5.

    Article  Google Scholar 

  29. Tautz, D. (1989) Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res 17, 6463–71.

    Article  PubMed  CAS  Google Scholar 

  30. Powell, W., Machray, G. C. and Provan, J. (1996) Polymorphism revealed by simple sequence repeats. Trends Plant Sci 1, 215–22.

    Google Scholar 

  31. Edwards, K. J., Barker, J. H. A., Daly, A., Jones, C., and Karp, A. (1996) Microsatellite libraries enriched for several microsatellite sequences in plants. Biotechniques 20, 758–60.

    PubMed  CAS  Google Scholar 

  32. Robinson, A. J., Love, C. G., Batley, J., Barker, G., and Edwards, D. (2004) Simple sequence repeat marker loci discovery using SSRPrimer. Bioinfomatics 20, 1475–6.

    Article  CAS  Google Scholar 

  33. Jewell, E., Robinson, A., Savage, D., Erwin, T., Love, C. G., Lim, G. A. C., Li, X., Batley, J., Spangenberg, G. C., and Edwards, D. (2006) SSR primer and SSR taxonomy tree: biome SSR discovery. Nucleic Acids Res 34, W656–9.

    Article  PubMed  CAS  Google Scholar 

  34. Abajian, C. (1994) SPUTNIK, http://abajian.net/sputnik/.

  35. Rozen, S., and Skaletsky, H. J. (2000) Primer3 on the WWW for general users and for biologist programmers, in: Bioinformatics Methods and Protocols: Methods in Molecular Biology (Krawetz S., and Misener S., Eds.), Humana Press, Totowa, NJ, pp 365–86.

    Google Scholar 

  36. Stajich, J. E., Block, D., Boulez, K., Brenner, S. E., Chervitz, S. A., Dagdigian, C., Fuellen, G., Gilbert, J. G. R., Korf, I., Lapp, H., Lehvaslaiho, H., Matsalla, C., Mungall, C. J., Osborne, B. I., Pocock, M. R., Schattner, P., Senger, M., Stein, L. D., Stupka, E., Wilkinson, M. D., and Birney, E. (2002) The Bioperl toolkit: Perl modules for the life sciences. Genome Res 12, 1611–8.

    Article  PubMed  CAS  Google Scholar 

  37. Wilson, I. D., Barker, G. L. A., Beswick, R. W., Shepherd, S. K., Lu, C., Coghill, J. A., Edwards, D., Owen, P., Lyons, R., Parker, J. S., Lenton, J. R., Holdsworth, M. J., Shewry, P. R., and Edwards, K. J. (2004) A transcriptomics resource for wheat functional genomics. Plant Biotechnol J 2, 495–506.

    Article  PubMed  Google Scholar 

  38. Green, P. (1994) Phrap, unpublished. www.phrap.org.

  39. Gordon, D., Abajian, C., and Green, P. (1998) Consed: a graphical tool for sequence finishing. Genome Res 8, 195–202.

    PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Australian Centre for Plant Functional Genomics, School of Land, Crop and Food Sciences, University of Queensland, Brisbane, Australia

    Jacqueline Batley & David Edwards

Authors
  1. Jacqueline Batley
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. David Edwards
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Dept. Bioquímica, Genética e Inmunología, Universidad de Vigo, Vigo, 36310, Spain

    David Posada

Rights and permissions

Reprints and permissions

Copyright information

© 2009 Humana Press, a part of Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Batley, J., Edwards, D. (2009). Mining for SNPs and SSRs Using SNPServer, dbSNP and SSR Taxonomy Tree. In: Posada, D. (eds) Bioinformatics for DNA Sequence Analysis. Methods in Molecular Biology, vol 537. Humana Press. https://doi.org/10.1007/978-1-59745-251-9_15

Download citation

  • DOI: https://doi.org/10.1007/978-1-59745-251-9_15

  • Published:

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-910-9

  • Online ISBN: 978-1-59745-251-9

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation