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- TITLE: Sequence Complexity of Chromosome 3 in Caenorhabditis elegans
- AUTHORS: Gaetano Pierro
JOURNAL NAME: Advances in Bioinformatics
Sep 16, 2014
- ABSTRACT: The nucleotide sequences complexity in chromosome 3 of Caenorhabditis elegans (C. elegans) is studied. The complexity of these sequences is compared with some random sequences. Moreover, by using some parameters related to complexity such as fractal dimension and frequency, indicator matrix is given a first classification of sequences of C. elegans. In particular, the sequences with highest and lowest fractal value are singled out. It is shown that the intrinsic nature of the low fractal dimension sequences has many common features with the random sequences. 1. Introduction The Caenorhabditis elegans (C. elegans) is a 1？mm length transparent nematode. Thanks to its simple organic structure, it was taken as a model for research into genetic field. Early studies on C. elegans began in 1962 with some works on cell lineage and apoptosis [1, 2]. There are 2 distinct sexual types of the C. elegans, the hermaphrodite and the male. The second one is very rarely represented in nature (being approximately only the 0.05% of the population). We have 959 cells in the hermaphroditic species and 1031 cells for the male. The sexual difference at the chromosomal level provides: XX chromosomes for hermafrodite and X0 for the male. The sexual reproduction of C. elegans is realized by 2 distinct pathways: mating or, in case of the hermaphrodite, by a self-fertilization. The life cycle of C. elegans consists of 4 larval stages (from L1 to L4); however, if there exists some hard environment conditions, such as lacking of food, the C. elegans remains in the L3 larval stage, until the conditions improve. The complete sequencing of C. elegans genome was completed in 2002. The C. elegans has 5 chromosomes autosomes plus the sex chromosome X. Totally, it is made up of nearly 100 million base pairs and 19000 genes [3–5]. Study on fractal analysis of multigenome of C. elegans has shown that chromosome 3 is the one with multifractal characteristics higher than the others, the less multifractal appears to be the chromosome sexual X . For the first time, in this work, we have analyzed the different types of sequences belonging to the genome of C. elegans, focusing our investigation on those that show fractal characteristics. Thus, chromosome 3 of C. elegans has been carefully studied because its unsymmetrical and inhomogeneous statistical characteristics. Through the analysis of this chromosome we can investigate what are the features that make it more “complex” from a biostatistical point of view and in particular with the use of statistical parameters such as the complexity, the