We have used in vitro selection techniques to characterize DNA sequences that are ligated efficiently by T4 RNA ligase. We find that the ensemble of selected sequences ligated about 10 times as efficiently as the random mixture of sequences used as the input for selection. Surprisingly, the majority of the selected sequences approximated a well-defined consensus sequence.

We have developed a program GAPE (Gap Allowing Pattern Explorer) to extract amino acid sequence motifs conserved among distantly related proteins. The GAPE program is designed to allow a gap in the sequences. When the program is applied to some ligand-related consensus sequences, motifs extracted with low expectation of occurrence contain some of the amino acid residues chemically proved to be ...