To isolate genes for new members of a protein family, it is frequently
necessary to design oligonucleotides on the basis of protein alignments.
DNAPROBE assists in the design of oligonucleotides in such cases. It
uses MSF protein alignments generated by the program PILEUP and codon
frequency tables from the Wisconsin (GCG) sequence analysis software
package. The basic algorithm calculates 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. Where an alignment
contains a cluster of closely related sequences, the user may choose to
implement a weighting option that reduces their individual contributions
to the output in order that they do not overwhelm the contributions of
more distantly related sequences which are under-represented. This may
be done in two ways; (a) 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 (b) by specifying weights in a
separate file which is then read by the program, an option which enables
one to give increased weight to sequences known to be more closely
related to the target organism.

根据蛋白序列对比设计核苷酸序列