PCAP - PROBE CHOICE AND ANALYSIS PACKAGE - A SET OF PROGRAMS TO AID IN CHOOSING SYNTHETIC OLIGOMERS FOR CONTIG MAPPING

In the program, PCAP, we provide a methodology for choosing synthetic oligonucleotide probes to be used in contig mapping experiments. The p ackage serves the purpose of presenting a series of short oligonucleot ides (8-12mers) that are chosen based on constraints with respect to f requency of occurrence within a particular genome and the G + C conten t of the oligonucleotides. The four programs contained within the pack age: (i) convert GenBank files to a format useable by the package; (ii ) calculate trinucleotide and tetranucleotide frequencies in available sequence data on a particular species; (iii) present the user with up per and lower bounds on the frequencies of hybridization sites for oli gonucleotide probes of length 8-12, (iv) allow the user to place const raints on site frequency and G + C content and provides a list of shor t probe sequences that fit these criteria. These sequences can then be synthetically produced and used in hybridization experiments to carry out contig mapping.