caa a22 4500 445821108 CHVBK 20180317145244.0 cr unu---uuuuu 170323e20110101xx s 000 0 eng 10.1007/s00239-010-9411-6 doi (NATIONALLICENCE)springer-10.1007/s00239-010-9411-6 Introns Form Compositional Clusters in Parallel with the Compositional Clusters of the Coding Sequences to Which they Pertain [Elektronische Daten] [Miguel Fuertes, José Pérez, Emile Zuckerkandl, Carlos Alonso] 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. Springer Science+Business Media, LLC, 2010 Human genome nationallicence Barcode nationallicence Genetic information nationallicence Intron nationallicence Exon nationallicence SD : Standard deviation nationallicence CDS : Coding sequence nationallicence IS : Intron sequence nationallicence Fuertes Miguel Centro de Biología Molecular "Severo Ochoa” (CSIC-UAM), Universidad Autónoma de Madrid, c/Nicolás Cabrera 1, 28049, Madrid, Spain aut Pérez José Bioapter S.L.c/Formentera, Polígono Industrial Las Rozas, Las Rozas, Madrid, Spain aut Zuckerkandl Emile Department of Biological Sciences, Stanford University, 94305, Stanford, CA, USA aut Alonso Carlos Centro de Biología Molecular "Severo Ochoa” (CSIC-UAM), Universidad Autónoma de Madrid, c/Nicolás Cabrera 1, 28049, Madrid, Spain aut Journal of Molecular Evolution Springer-Verlag 72/1(2011-01-01), 1-13 0022-2844 72:1<1 2011 72 239 https://doi.org/10.1007/s00239-010-9411-6 text/html Onlinezugriff via DOI 1 research-article jats NATIONALLICENCE 856 40 https://doi.org/10.1007/s00239-010-9411-6 text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Fuertes Miguel Centro de Biología Molecular "Severo Ochoa” (CSIC-UAM), Universidad Autónoma de Madrid, c/Nicolás Cabrera 1, 28049, Madrid, Spain aut NATIONALLICENCE 700 1- Pérez José Bioapter S.L.c/Formentera, Polígono Industrial Las Rozas, Las Rozas, Madrid, Spain aut NATIONALLICENCE 700 1- Zuckerkandl Emile Department of Biological Sciences, Stanford University, 94305, Stanford, CA, USA aut NATIONALLICENCE 700 1- Alonso Carlos Centro de Biología Molecular "Severo Ochoa” (CSIC-UAM), Universidad Autónoma de Madrid, c/Nicolás Cabrera 1, 28049, Madrid, Spain aut NATIONALLICENCE 773 0- Journal of Molecular Evolution Springer-Verlag 72/1(2011-01-01), 1-13 0022-2844 72:1<1 2011 72 239 Metadata rights reserved Springer special CC-BY-NC licence nationallicence BK010053 XK010053 XK010000 NATIONALLICENCE NATIONALLICENCE NL-springer