Oligonucleotide based microarrays offer both technical and functional
advantages over cDNA based microarrays. The ability to produce
microarrays without extensive cDNA clone libraries and without PCR is
a technical advantage to the researcher. Also, oligonucleotide
microarrays offer the ability to design features that will distinguish
between differentially spliced mRNAs and even single nucleotide
polymorphisms(SNPs). However, it is first necessary to decide on the
sequences that will give optimal hybridization results for the genes
of interest. Here we describe a program which attempts to automate the
selection of an optimal oligonucleotide probe given the sequence of a
gene. This program, oligoPicker, takes into consideration a number of
factors including: melting temperature, secondary structure, and
homology of the probe to other genes in the database.
