GENEUP - A PROGRAM TO SELECT SHORT PCR PRIMER PAIRS THAT OCCUR IN MULTIPLE MEMBERS OF SEQUENCE LISTS

A computer program is presented that selects a small set of short prim er pairs for PCR to sample all the sequences in a user-specified list of mRNAs. Such primer pairs could be used to increase the probability of sampling mRNAs of particular interest in differential display and t o generate simplified hybridization probes for DNA chips or arrays. Th e program uses simulated PCR to find pairs of primers that sample more than one sequence in the list. A small set of such primer pairs is se lected that give maximal coverage of the sequences in the list. Primer pairs are excluded that: (i) generate simulated PCR products of the s ame size from a number sequences irt the list, (ii) can easily form pr imer dimers, (iii) are outside a specified range of G + C content or ( iv) occur in another list of undesirable sequences, such as rRNAs and Alu repeats. Five lists consisting of from 48-285 cDNA sequences were used to test the program. A small number of pairs of primers, 8-10 bas es in length, were selected that fit the above criteria and that gener ate one or more simulated PCR products in all or most of the cDNAs in each list.