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


BACKGROUND
available on request from the authors.


METHODS
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. Supplementary data is available at Bioinformatics online.
Yang
Guojun
G
Institute of Developmental and Molecular Biology, Department of Biology, Texas A&M University, College Station, TX 77843, USA.
Hall
Timothy C
TC
D000465:Algorithms; D017360:Arabidopsis / Q000235:genetics*; D002874:Chromosome Mapping / Q000379:methods*; D018745:Genome, Plant / Q000235:genetics*; D023281:Genomics / Q000379:methods; D015183:Restriction Mapping / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D019076:Transgenes / Q000235:genetics*