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Bioinformatics Vol. 18 no. 11 2002
Pages 1410-1417
© 2002 Oxford University Press

ARROGANT: an application to manipulate large gene collections

Amit V. Kulkarni 1, Noelle Sevilir Williams 7, Yun Lian 5,6, Jonathan D. Wren 2, David Mittelman 5,6, Alexander Pertsemlidis 4,5 and Harold R. Garner 3,4,5,6,*

1 Program in Biomedical Engineering
2 Program in Genetics and Development, Southwestern Graduate School of Biomedical Science
3 Department of Biochemistry
4 Department of Internal Medicine
5 McDermott Center for Human Growth and Development
6 Center for Biomedical Inventions
7 Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA

Received on February 2, 2002 ; revised on April 10, 2002 ; accepted on April 20, 2002

Summary: ARROGANT (ARRay OrGANizing Tool) is a software tool developed to facilitate the identification, annotation and comparison of large collections of genes or clones. The objective is to enable users to compile gene/clone collections from different databases, allowing them to design experiments and analyze the collections as well as associated experimental data efficiently. ARROGANT can relate different sequence identifiers to their common reference sequence using the UniGene database, allowing for the comparison of data from two different microarray experiments. ARROGANT has been successfully used to analyze microarray expression data for colon cancer, to compile genes potentially related to cardiac diseases for subsequent resequencing (to identify single nucleotide polymorphisms, SNPs), to design a new comprehensive human cDNA microarray for cancer, to combine and compare expression data generated by different microarrays and to provide annotation for genes on custom and Affymetrix chips.

Availability: ARROGANT is freely available for use on the web at http://lethargy.swmed.edu/

Contact: harold.garner{at}utsouthwestern.edu

* To whom correspondence should be addressed.


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