Similarity in Oligonucleotide Usage in Introns and
Intergenic Regions Contributes to Long Range
Correlation in the Caenorhabditis elegans Genome
Clara Frontali and Elisabetta Pizzi,
Laboratory of Cell Biology, Istituto Superiore di Sanita,
Viale Regina Elena 299, Rome, Italy.
e-mail:
frontali@iss.infn.it
Gene , 232:87-95 (1999)
Abstract
A method is presented which allows detection of a sequence correlation
effect not related to patchiness in base composition or to preferences in
codon usage. Recurrence plots providing local views of oligonucleotide
recurrence regimen show that introns and intergenic regions are often
characterised by a highly recurrent use of oligonucleotides. By window
analysis it is possible to score a long sequence for the recurrence of a
given subset of oligos while filtering away the effects of short range
correlations. Long range exploration of chromosome III from
Caenorhabditis elegans reveals that consistent use of
recurrent oligonucleotides in introns and intergenic regions generates
a correlation effect that extends over several megabases.
