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Researchers pursuing the cloning of novel genes are ofte n faced with the problem that only a partial protein sequence i s known. Several procedures are commonly used involving th e reverse translation of the protein sequence into a DNA s e quence. These include synthesis of a short oligonucleotide s e quence for screening libraries and of a primer pair for ampl i fication of target sequence by polymerase chain reactio n (PCR). However, due to redundancy in the genetic code , oligonucleotide design must account for ambiguous DNA bases. When a protein sequence is reverse-translated, the r e sulting DNA sequence frequently contains as high as 50% ambiguous bases. This requires that primers be designed from regions of lower degeneracy. Manual location of such primer s is a tedious process and often fails due to the presence of se c ondary structures. Primer Premier automatically scans the ta r get DNA sequences and designs primers in regions of low d e generacy that are free of secondary structures, includin g hairpins, dimers and false priming sites. These primers ar e checked for the overall percentage of ambiguous bases a s well as the number of ambiguous bases occurring at the crit i cal 3 ′ end. We report here successful amplification of a gen e with the primers designed from its protein sequence using th e Primer Premier primer design program .