Similarity in oligonucleotide usage in introns and intergenic regions contributes to long-range correlation in the Caenorhabditis elegans genome.
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.
Frontali
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Laboratory of Cell Biology, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy. frontali@iss.infn.it
Pizzi
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D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics*; D019295:Computational Biology / Q000379:methods; D016678:Genome; D007438:Introns; D009838:Oligodeoxyribonucleotides / Q000235:genetics*; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
D009838:Oligodeoxyribonucleotides