allows you to design oligonucleotides in order to isolate genes for new members of a protein family. To isolate genes for new members of a protein family, it is frequently necessary to design oligonucleotides on the basis of protein alignments.
The program uses MSF protein alignments generated by the PILEUP utility as well as codon frequency tables from the Wisconsin (GCG) sequence analysis software application.
The basic algorithm computes the most probable nucleotide sequence corresponding to the alignment by summing the products of the frequency with which a particular amino acid occurs at any one position, and the codon usage frequency for that amino acid.
You can select to implement a weighting option where an alignment contains a cluster of closely related sequences, which reduces their individual contributions to the output in order that they do not overwhelm the contributions of more distantly related sequences that are under-represented.
This can be accomplished in two ways: (1) using the algorithm of Gerstein et al. (J. Mol. Biol., 236, 1067-1078) and the information contained in the dendrogram file written by PILEUP, or (2) by specifying weights in a separate file which is then read by the program, an option which enables you to give increased weight to sequences known to be more closely related to the target organism.