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Bioinformatics Advance Access published online on December 15, 2005
Bioinformatics, doi:10.1093/bioinformatics/btk003
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received July 13, 2005
Revised December 8, 2005
Accepted December 11, 2005

Article

HideNseek, a post-genome approach to locate transgenes exemplified in Arabidopsis thaliana

Guojun Yang 1 and Timothy C. Hall 2 *

1 Institute of Developmental and Molecular Biology and Department of Biology, Texas A&M University, College Station, TX 77843-3155, USA; currently at: Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
2 Institute of Developmental and Molecular Biology and Department of Biology, Texas A&M University, College Station, TX 77843-3155, USA

* To whom correspondence should be addressed.
Timothy C. Hall, E-mail: tim{at}idmb.tamu.edu


  Abstract

Summary: Determination of transgene location is essential for investigating the effects of position on transgene expression levels and facilitates cloning of the resident gene affected by the insertion. Currently used PCR-based approaches for determination of transgene location are relatively complicated and often fail when the transgene is duplicated, rearranged or fragmented. HideNseek is a new bioinformatics tool that allows computation of transgene locations, provided that a suitable genomic restriction enzyme digestion profile is available. Since the new approach is not based on the terminal sequences of the transgene insert, it is less sensitive to transgene duplication, rearrangement or fragmentation. HideNseek has been tested experimentally and by in silico simulation. The experimental example provided here shows that this simple approach is feasible, permitting rapid location of transgenes with little bench work.

Availability: available on request from the authors.

Supplementary data: HideNseek input and output examples, experimental procedures and figures showing experimental results are provided as supplementary files: Supplementary material 1, 2, 3, and Supplementary figures (Figs 1 and 2), respectively.


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