6. SNP Discovery through EST Data Mining

  1. Zhanjiang (John) Liu
  1. Shaolin Wang and
  2. Zhanjiang (John) Liu

Published Online: 10 DEC 2010

DOI: 10.1002/9780470958964.ch6

Next Generation Sequencing and Whole Genome Selection in Aquaculture

Next Generation Sequencing and Whole Genome Selection in Aquaculture

How to Cite

Wang, S. and Liu, Z. (2011) SNP Discovery through EST Data Mining, in Next Generation Sequencing and Whole Genome Selection in Aquaculture (ed Z. (. Liu), Wiley-Blackwell, Oxford, UK. doi: 10.1002/9780470958964.ch6

Editor Information

  1. The Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849 USA

Author Information

  1. The Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849 USA

Publication History

  1. Published Online: 10 DEC 2010
  2. Published Print: 28 JAN 2011

ISBN Information

Print ISBN: 9780813806372

Online ISBN: 9780470958964

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Keywords:

  • SNP discovery through EST data mining;
  • key issue of single-nucleotide polymorphism (SNP) marker applications - in aquaculture species, availability of SNPs;
  • SNP discovery through EST data mining - advantages and disadvantages;
  • EST-derived SNPs - correlating genes in terms of genomic locations;
  • SNP discovery using ESTs - generated by Sanger sequencing;
  • SNP discovery using EST, alignment of multiple EST sequences - from a single transcript;
  • multiple alignment tool, The ClustalX/ClustalW program - for protein and nucleic acid multiple sequence alignments and phylogenetic tree construction;
  • identification of SNP using ClustalW - and NCBI BLAST;
  • transcript sequences, using next generation sequencing platforms - as Illumina Genome Analyzer and Roche 454 sequencer;
  • CLC Genomics Workbench, package - integrating analysis functions for nucleotide and protein sequences, as sequence assembly

Summary

This chapter contains sections titled:

  • Advantages and Disadvantages of SNP Discovery through EST Data Mining

  • SNP Discovery Using ESTs Generated by Sanger Sequencing

  • SNP Discovery Using Transcript Sequences Generated by Next Generation Sequencing

  • Windows - Based Platforms for EST Assembly and SNP Identification

  • Summary

  • References