Computer selection of oligonucleotide probes from amino acid sequences for use in gene library screening

Abstract

We present a computer program, FINPROBE, which utilizes known amino acid sequence data to deduce minimum redundancy oligonucleotide probes for use in screening cDNA or genomic libraries or in primer extension. The user enters the amino acid sequence of interest, the desired probe length, the number of probes sought, and the constraints on oligonucleotide synthesis. The computer generates a table of possible probes listed in increasing order of redundancy and provides the location of each probe in the protein and mRNA coding sequence. Activation of a next function provides the amino acid and mRNA sequences of each probe of interest as well as the complementary sequence and the minimum dissociation temperature of the probe. A final routine prints out the amino acid sequence of the protein in parallel with the mRNA sequence listing all possible codons for each amino acid.

Using Synthetic Oligonucleotides as Probes

“…In addition, three of the commonest amino acids have a total of six different codons each (see codon chart, APPENDIX 1). Computer programs are available to determine the optimal structure of oligonucleotide probes from amino acid sequences (Yang et al, 1984).…”

BIGPROBE: a computer program that predicts the sequence of long oligonucleotide probes with high reliability

“…Several computer programs have been described to aid in selection of nucleic acid probes based on amino acid sequence (16)(17)(18), but they are intended for use with short probe lengths. They make use of knowledge of the redundancy in the genetic code to select stretches of coding sequence with relatively low ambiguity.…”