Introns Form Compositional Clusters in Parallel with the Compositional Clusters of the Coding Sequences to Which they Pertain |
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Authors: | Miguel A Fuertes José M Pérez Emile Zuckerkandl Carlos Alonso |
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Affiliation: | 1.Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM),Universidad Autónoma de Madrid,Madrid,Spain;2.Bioapter S.L.c/Formentera, Polígono Industrial Las Rozas,Madrid,Spain;3.Department of Biological Sciences,Stanford University,Stanford,USA;4.Institute of Molecular Medical Sciences,Stanford,USA |
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Abstract: | This report deals with the study of compositional properties of human gene sequences evaluating similarities and differences
among functionally distinct sectors of the gene independently of the reading frame. To retrieve the compositional information
of DNA, we present a neighbor base dependent coding system in which the alphabet of 64 letters (DNA triplets) is compressed
to an alphabet of 14 letters here termed triplet composons. The triplets containing the same set of distinct bases in whatever
order and number form a triplet composon. The reading of the DNA sequence is performed starting at any letter of the initial
triplet and then moving, triplet-to-triplet, until the end of the sequence. The readings were made in an overlapping way along
the length of the sequences. The analysis of the compositional content in terms of the composon usage frequencies of the gene
sequences shows that: (i) the compositional content of the sequences is far from that of random sequences, even in the case
of non-protein coding sequences; (ii) coding sequences can be classified as components of compositional clusters; and (iii)
intron sequences in a cluster have the same composon usage frequencies, even as their base composition differs notably from
that of their home coding sequences. A comparison of the composon usage frequencies between human and mouse homologous genes
indicated that two clusters found in humans do not have their counterpart in mouse whereas the others clusters are stable
in both species with respect to their composon usage frequencies in both coding and noncoding sequences. |
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