Phylarray is a program for designing oligonucleotide probes (from 16S rRNA) for use in phylogenetic microarray experiments.
Phylarray allows the design of highly specific probes that target 16S bacterial rRNA. It uses the Ribosomal Database Project as a sequence database, and performs an original algorithm to find probes that best identify any bacterial group. For the moment, PhylArray only allows identifying genus but soon it will be able to work at any level of the phylogenetic tree.
The user specifies the bacterial genus he wants to identify and the required oligonucleotide length (20-70 mers), and specificity parameters. When computation is finished, he receives an email that indicates where to find the results. The latter consist of a list of probe sequences with possible cross-hybridizations.
Due to the algorithm particularities, one probe consists of a sequence with degenerate bases, and the list of effective sequences (with "real" bases) that target the required bacteria.