BioPerlTutorial_final.pdf

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Using Bioinformatics to Identify Promoters in
Genome Sequences
Carlos M. Hernandez-Garcia and Gabriel Abud
Department of Horticulture and Crop Science, OARDC/The Ohio
State University, 1680 Madison Ave., Wooster, OH 44691, USA
hernandez-garcia.1@buckeyemail.osu.edu
Purpose of this tutorial
Provide step-by-step instructions to
automatically identify DNA sequences in a genome
sequence using a BioPerl script
Rationale
With
the continual release of plant genome sequences,
the accumulation of genomics information has been
exponentially increasing
Automated analysis and mining of genome databases
is becoming essential and routine due to the volume of
data
Biological rationale for targeting promoters
Promoters
are DNA sequences located in front of gene
coding sequences
Due
to their influence on gene expression, promoters are of
interest as tools to regulate Genetically Modified Organism
(GMO) products and as markers for natural variation
Promoters
with different functionality in terms of
inducibility, tissue specificity, strength etc. are needed
In
this tutorial, we will focus on the identification of
ubiquitin promoters of tomato which drive strong gene
expression in important crops such as maize (Christensen
and Quail 1996), rice (Sivamani and Qu 2006), potato
(Garbarino et al. 1995), tomato (Rollfinke et al. 1998) and
soybean (Hernandez-Garcia et al. 2009)
Specific objective:
To identify
ubiquitin
genes and their promoter sequences in
a draft genome of tomato using a BioPerl script in a
Windows operating system

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