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 package serves the purpose of presenting a series of short oligonucleotides (8-12mers) that are chosen based on constraints with respect to frequency of occurrence within a particular genome and the G+C content of the oligonucleotides. The four programs contained within the package: (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 upper and lower bounds on the frequencies of hybridization sites for oligonucleotide probes of length 8-12, (iv) allow the user to place constraints on site frequency and G+C content and provides a list of short probe sequences that fit these criteria. These sequences can then be synthetically produced and used in hybridization experiments to carry out contig mapping.