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Bioinformatics Vol. 19 no. 14 2003
Pages 1846-1848
© 2003 Oxford University Press

Applications Note

A tool-kit for cDNA microarray and promoter analysis

N. H. Shah 1,*, D. C. King 1, P. N. Shah 2 and N. V. Fedoroff 1

1 The Huck Institute of Life Sciences and 2 The Department of Biology, Pennsylvania State University, University Park, PA 16802, USA

Received on February 10, 2003 ; revised on April 1, 2003 ; accepted on April 4, 2003

We describe two sets of programs for expediting routine tasks in analysis of cDNA microarray data and promoter sequences. The first set permits bad data points to be flagged with respect to a number of parameters and performs normalization in three different ways. It allows combining of result files into comprehensive data sets, evaluation of the quality of both technical and biological replicates and row and/or column standardization of data matrices. The second set supports mapping ESTs in the genome, identifying the corresponding genes and recovering their promoters, analyzing promoters for transcription factor binding sites, and visual representation of the results. The programs are designed primarily for Arabidopsis thaliana researchers, but can be adapted readily for other model systems.

Availability and Supplementary information: http://www.personal.psu.edu/nhs109/Programs/

Contact: nigam{at}psu.edu

* To whom correspondence should be addressed.


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