Other Species

Designing Software to Locate Differences in the Shrimp Genome

  • Danielle M. Bowen (Iowa State University)
  • Zhi-Liang Hu (Iowa State University)
  • Zhi-Qiang Du (Iowa State University)
  • Max F. Rothschild (Iowa State University)


In order to determine where important differences in the genomic sequence of Pacific White Shrimp occur, many copies each of multiple regions of DNA sequence are needed. Then similar sequences can be aligned so that almost all of the bases are identical between the sequences and differences are easy to notice. One of the major issues with predicting single base position differences (SNPs) in this manner is that DNA sequencing techniques are not 100% consistent in most cases. Consequently, it needs to be determined whether a particular base is different because the true genetic sequence is variable at that position or because the sequencing process resulted in the base position being incorrectly called. SNPidentifier is a newly developed computer program that takes into account the unreliability of sequence data and tries to use only the more reliable sequences to predict where true SNPs are located. The goal of locating SNPs in Pacific White Shrimp is to identify base positions that can possibly be used in the future as molecular markers for traits of interest to shrimp breeders.

Keywords: ASL R2353

How to Cite:

Bowen, D. M., Hu, Z., Du, Z. & Rothschild, M. F., (2008) “Designing Software to Locate Differences in the Shrimp Genome”, Iowa State University Animal Industry Report 5(1). doi: https://doi.org/10.31274/ans_air-180814-872

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Published on
01 Jan 2008