However, the use of DNA microarrays for routine applications produces many challenges for bioinformatics. Firstly, probe selection is a difficult and time consuming process. There are a huge number of diverse species in nature, of which we have sequence information for only a tiny fraction. This makes it difficult to find oligonucleotides, either alone or in combination, that uniquely identify species of interest. Oligos may have homology to multiple species, which results in a complex and noisy hybridization pattern. Secondly, each nucleic acid sample tested will typically contain a mixture of DNA and RNA from the organism of interest, the host and from a variety of contaminants, which may all contribute to the resulting microarray profile. Furthermore, this may be complicated by the presence of multiple, possibly related, pathogen species, making it difficult to separate patterns due to cross-hybridization from a true positive result.