Ribosomal DNA internal transcribed spacer (ITS) sequences were investigated in the genera Alternaria, Aspergillus, Cladosporium and Penicillium, to identify regions suitable for the design of genus- and species-specific oligonucleotide probes. The ITS regions of all four genera were quite distinct. However, we discovered that the genera Aspergillus and Penicillium displayed high similarity in most of the ITS2 region. Whilst interspecies similarity within Alternaria and Cladosporium was high in both ITS regions 1 and 2, ITS1 similarity within Aspergillus and Penicillium was lower by comparison. We conclude that: (1) the ITS2 region is highly conserved between Aspergillus and Penicillium, and (2) the ITS1 region will allow for the development of specific probes to distinguish between Aspergillus and Penicillium.
The immense number of nucleotide and protein sequences that can be accessed through public databases on the Internet is an invaluable resource to scientists working in the fields of molecular biology, protein chemistry and molecular diagnostics. Tools such as BLAST (1) (also discussed in the March 2000 Internet On-Ramp) and FASTA ( 7) are used mainly to search for database sequences that are similar or potentially homologous to query sequences supplied by the investigator. However, in many circumstances, this is only the first stage of a more complex series of sequence analyses. Multiple sequence alignment analyses are fundamental in allowing investigators to draw conclusions about the similarity, function, structure and the potential evolutionary relationships between sequences. This column will focus on a number of different multiple sequence alignment tools available as services over the Web.
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