BioPerl Tutorial: Extracting DNA Sequences From a Database


Carlos Hernandez Garcia, The Ohio State University; Gabriel Abud, The Ohio State University

This tutorial helps users extract DNA sequences of interest from a database using a BioPerl script by providing the example of extracting ubiquitin promoter sequences from a draft of the tomato genome sequence. The tutorial includes instructions, explanations, and screenshots in powerpoint and word document formats. The BioPerl script is also included.

In the event that the slideshare tutorial does not work, the tutorial is also attached as a pdf at the bottom of the page.

References Cited

  • Christensen A. H., and P. H. Quail. 1996. Ubiquitin promoter-based vectors for high levels of selectable and/or screenable marker genes in monocotyledonous plants. Transgenic Research 5: 213–218. (Available online at: (verified 11 May 2012).
  • Garbarino, J. E., T. Oosumi, and W. R. Belknap. 1995. Isolation of a polyubiquitin promoter and its expression in transgenic potato plants. Plant Physiology 109: 1371–1378. (Available online at: (verified 11 May 2012).
  • Hernandez-Garcia, C. M., R. A. Bouchard, P. J. Rushton, M. L. Jones, X. Chen, M. P. Timko, and J. J. Finer. 2010b. High level transgenic expression of soybean (Glycine max) GmERF and Gmubi gene promoters isolated by a novel promoter analysis pipeline. BMC Plant Biology 10: 237. (Available online at: (verified 11 May 2012).
  • Hernandez-Garcia, C. M., J. M. Chiera, and J. J. Finer. 2010a. Robotics and dynamic image analysis for studies of gene expression in plant tissues. Journal of Visualized Experiments 39. (Available online at: (verified 11 May 2012).
  • Hernandez-Garcia, C. M., A. P. Martinelli, R. A. Bouchard, and J. J. Finer. 2009. A soybean (Glycine max) polyubiquitin promoter gives strong constitutive expression in transgenic soybean. Plant Cell Reports 28: 837-849. (Available online at: (verified 11 May 2012).
  • Rollfinke, I. K., M. V. Silber, and U. M. Pfitzner. 1998. Characterization and expression of a heptaubiquitin gene from tomato. Gene 211: 267–276. (Available online at: (verified 11 May 2012).
  • Sivamani, E. and R. Qu. 2006. Expression enhancement of a rice polyubiquitin gene promoter. Plant Molecular Biology 60: 225–239. (Available online at: (verified 11 May 2012).

External Links

Additional Resources

  • The Perl programming language [Online]. Available at: (verified 11 May 2012).

The following are relatively non-technical resources for learning Perl

  • Medinets, D. 1996. Perl 5 by example. Que, Indianapolis, IN.
  • Siever, E., and S. Spainhour. 2002. Perl in a nutshell. O’Reilly Media, Sebastopol, CA.

Funding Statement

Development of this lesson was supported in part by the National Institute of Food and Agriculture (NIFA) Solanaceae Coordinated Agricultural Project, agreement 2009-85606-05673, administered by Michigan State University, The Ohio State University Department of Horticulture and Crop Science, Ohio Research Internship Project (ORIP), and CONACYT, Mexico. Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the United States Department of Agriculture or any of the other aforementioned entities.

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