title: The exceptional genomic word symmetry along DNA sequences.
abstract: BACKGROUND
  The second Chargaff's parity rule and its extensions are recognized as universal phenomena in DNA sequences. However, parity of the frequencies of reverse complementary oligonucleotides could be a mere consequence of the single nucleotide parity rule, if nucleotide independence is assumed. Exceptional symmetry (symmetry beyond that expected under an independent nucleotide assumption) was proposed previously as a meaningful measure of the extension of the second parity rule to oligonucleotides. The global exceptional symmetry was detected in long and short genomes.
  
  
  RESULTS
  To explore the exceptional genomic word symmetry along the genome sequences, we propose a sliding window method to extract the values of exceptional symmetry (for all words or by word groups). We compare the exceptional symmetry effect size distribution in all human chromosomes against control scenarios (positive and negative controls), testing the differences and performing a residual analysis. We explore local exceptional symmetry in equivalent composition word groups, and find that the behaviour of the local exceptional symmetry depends on the word group.
  
  
  CONCLUSIONS
  We conclude that the exceptional symmetry is a local phenomenon in genome sequences, with distinct characteristics along the sequence of each chromosome. The local exceptional symmetry along the genomic sequences shows outlying segments, and those segments have high biological annotation density.
authors: Department of Mathematics, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal. vera@ua.pt.|Department of Medical Sciences and Institute of Biomedicine - iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal, Campus Universitário de Santiago, Aveiro, Portugal. vera@ua.pt.|IEETA-Institute of Electronic Engineering and Informatics of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal. vera@ua.pt.
authors: Vera
authors: V
authors: Afreixo
authors: Department of Electronics, Telecommunications and Informatics, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal. cbastos@ua.pt.|IEETA-Institute of Electronic Engineering and Informatics of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal. cbastos@ua.pt.
authors: João M O S
authors: JM
authors: Rodrigues
authors: Department of Electronics, Telecommunications and Informatics, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal. cbastos@ua.pt.|IEETA-Institute of Electronic Engineering and Informatics of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal. cbastos@ua.pt.
authors: Carlos A C
authors: CA
authors: Bastos
authors: Department of Medical Sciences and Institute of Biomedicine - iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal, Campus Universitário de Santiago, Aveiro, Portugal. raquelsilva@ua.pt.|IEETA-Institute of Electronic Engineering and Informatics of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal. raquelsilva@ua.pt.
authors: Raquel M
authors: RM
authors: Silva
mesh_terms: D002877:Chromosomes, Human / Q000235:genetics*; D004247:DNA / Q000235:genetics*; D015894:Genome, Human; D023281:Genomics; D006801:Humans; D008957:Models, Genetic; D015233:Models, Statistical; D059467:Transcriptome
chemical_list: D004247:DNA