Oliz, a suite of Perl scripts that assist in the design of microarrays using 50mer oligonucleotides from the 3′ untranslated region

Abstract

Background: Identifying reliable oligonucleotide sequences for use in microarray experiments is a complex process. Two key issues are the accuracy of the input sequences and the specificity of the oligonucleotide sequences. Results: We provide a suite of Perl scripts that facilitates the search for gene-specific oligonucleotides for microarray experiments. Genes of interest are first identified in the form of UniGene clusters. The sequences of these clusters were extracted and assembled into contigs to increase their accuracy. The 3′ untranslated region (3′ UTR) of the contig was parsed. Then, multiple 50mer oligonucleotide sequences with similar melting temperature were obtained from each 3′UTR. These sequences were analyzed for gene specificity. Five Cy3-labeled cDNAs were used to empirically verify the specificity of a set of 1814 50mers. Conclusion: Oliz can be used to select oligonucleotide sequences for microarrays. Oliz is freely available for academic users at [http://www.utmem.edu/pharmacology/otherlinks/oliz.html] © 2002 Chen and Sharp; licensee BioMed Central Ltd.