Distance analysis helps to establish characteristic motifs in intron sequences.
Computer-assisted sequence analysis was applied to detect the most apparent nonrandom sequence motifs in eukaryotic introns. We describe in detail a method, which we call distance analysis, that we applied to the extensive study of 405 eukaryotic intron sequences. We observed very strong two-base periodicities for almost all tetranucleotides that are tandem repeats of nonhomopolymeric dinucleotides (the exception was GCGC and CGCG). We also observed, by using a fixed-point alignment method, that these periodic sequence motifs belong to large clusters of dinucleotides repeated tandemly as many as 15-35 times, which corresponds to the cluster lengths of 30-70 bases. We did not observe two-base periodicity of tetranucleotides in the collections of either 262 spliced eukaryotic exons or 107 bacterial genes. Instead, these sequences displayed strong three-base periodicity of some other tetranucleotides. These findings suggest that introns and exons display distinct sequence properties that can be used for mapping purposes.
Konopka
A K
AK
National Cancer Institute, Frederick, Maryland 21701-1013.
Smythers
G W
GW
Owens
J
J
Maizel
J V
JV
D001483:Base Sequence; D005091:Exons; D005798:Genes, Bacterial; D005821:Genetic Techniques; D007438:Introns; D009843:Oligoribonucleotides
D009843:Oligoribonucleotides