THE GPRIME PACKAGE - COMPUTER-PROGRAMS FOR IDENTIFYING THE BEST REGIONS OF ALIGNED GENES TO TARGET IN NUCLEIC-ACID HYBRIDIZATION-BASED DIAGNOSTIC-TESTS, AND THEIR USE WITH PLANT-VIRUSES

The GPRIME (Group PRIMEr design) programs examine aligned sets of gene sequences to discover homologous regions to be targeted in diagnostic tests. The core program moves a 'window' over the aligned sequences a nd calculates, at each window position, a 'redundancy value', namely t he number of sequences that would represent all permutations of the va riable sequence positions within that window. Regions with minimal red undancy values may then be targeted in diagnostic tests based on oligo nucleotide hybridisation. The likely specificity of tests targeting su ch regions can be assessed by searching the international databases wi th those regions using FASTA. The GPRIME programs, which include progr ams for designing primers to distinguish between two sub-sets of a gro up of aligned sequences, can be obtained from http://life.anu.edu.au/s oftware.html. We have used GPRIME to design redundant primers for RT-P CR tests to detect all potexviruses and tobamoviruses, and then used t hese, together with a previously reported pair of primers for the Poty viridae, to screen some Australian orchid collections. Two orchid viru ses previously reported from Australia were found; cymbidium mosaic po texvirus was common, but odontoglossum ringspot tobamovirus was not. I n addition the recently described ceratobium mosaic potyvirus was foun d to be common, and three other novel potyviruses were also found. (C) 1998 Elsevier Science B.V. All rights reserved.