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...
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| Veröffentlicht in: | Gene 1999-05, Vol.232 (1), p.87-95 |
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| container_title | Gene |
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| creator | Frontali, Clara Pizzi, Elisabetta |
| description | 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. |
| doi_str_mv | 10.1016/S0378-1119(99)00111-0 |
| format | Article |
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| fulltext | fulltext |
| identifier | ISSN: 0378-1119 |
| ispartof | Gene, 1999-05, Vol.232 (1), p.87-95 |
| issn | 0378-1119 1879-0038 |
| language | eng |
| recordid | cdi_proquest_miscellaneous_69766655 |
| source | MEDLINE; Elsevier ScienceDirect Journals |
| subjects | Animals Caenorhabditis elegans Caenorhabditis elegans - genetics Computational Biology - methods Correlation structure Genome Genome organisation Introns Non-coding DNA Oligodeoxyribonucleotides - genetics Recurrence sequence analysis Repetitive Sequences, Nucleic Acid - genetics Sequence Analysis, DNA - methods Software |
| title | Similarity in oligonucleotide usage in introns and intergenic regions contributes to long-range correlation in the Caenorhabditis elegans genome |
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