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 pe...

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Bibliographic Details
Published inGene analysis techniques and applications Vol. 4; no. 4; pp. 63 - 74
Main Authors Konopka, A.K, Smythers, G.W, Owens, J, Maizel, J.V. Jr
Format Journal Article
LanguageEnglish
Published 1987
Subjects
computer analysis
computer techniques
dinucleotides
DNA
intervening sequences
introns
nucleotide sequences
nucleotides
oligonucleotides
repetitive dinucleotides
repetitive sequences
sequence alignment
tetranucleotides
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Summary: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.
ISSN:0735-0561