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© Oxford University Press

PCAP: probe choice and analysis package—a set of programs to aid in choosing synthetic oligomers for contig mapping

A.J. Cuticchia , J. Arnold 1,2 and W.E. Timberlake 1

Genome Database, Welch Medical Library, The Johns Hopkins School of Medicine 1830 East Monument Street, Baltimore, MD 21205
1Department of Genetics, The University of Georgia Athens, GA 30602, USA

2To whom reprint requests should be sent

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; (iv) 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.

Received on April 26, 1992; accepted on July 15, 1992

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Nucleic Acids Res., July 26, 2005; 33(13): e115 - e115.
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