The breakdown of the word symmetry in the human genome

Persistence and breakdown of strand symmetry in the human genome

“…It is well symmetric for its frequency framework in terms of at least mononucleotides. The symmetry index based on the L 1 distance (Baisnée et al, 2002; calculated as 1 À S 1 in Afreixo et al (2013)) for mononucleotides is 0.9831 for this sequence. The value of the symmetry index is sufficiently high because the highfrequency mononucleotides (A and T) are perfectly symmetric.…”

“…The results of Qi and Cuticchia (2001) would not be conclusive because only some pairs of complementary decanucleotides were analyzed. Afreixo et al (2013) analyzed the word symmetry (strand symmetry) in the human genome in terms of mononucleotides through decanucleotides. They performed an extensive survey, analyzing the situations of all the complementary oligonucleotide pairs.…”

“…It was from these approaches, but not others also employed, that they drew their conclusion. From the equivalence tests ( Table 2 in Afreixo et al (2013)), it is clear that the percentages of equivalent (i.e., statistically significant) complementary oligonucleotide pairs in the human genome are all 100% as long as the order of oligonucleotides is r6 (for δ¼1.1) or r7 (for δ¼ 1.3). Therefore, Contents lists available at ScienceDirect journal homepage: www.elsevier.com/locate/yjtbi in their opinion, the symmetry level is no longer statistically significant for oligonucleotides 46 nt.…”

“…Also, the putative genomes are characterized by the considerable differences in terms of frequencies of complementary oligonucleotides. From the data in Afreixo et al (2013, Table 2 and Table 3), it may be worked out that in such a putative genome even if the ratio between the frequencies of complementary oligonucleotides of 6 nt is as large as 1.05 (or as small as its reciprocal 0.95, similarly hereafter) for all the complementary pairs (excluding the oligonucleotide whose reverse complement is itself), 100% of the complementary hexanucleotide pairs pass the equivalence tests (the choice of hexanucleotides, but not oligonucleotides of higher order, in this example is to ensure that the occurrence of every oligonucleotide concerned is sufficiently abundant so that every pair of complementary hexanucleotides, even with a frequency ratio of 1.05, is an equivalent one). Nevertheless, the symmetry index for hexanucleotides of the genome is only 0.9756 in this situation.…”

Attaining the 2nd Chargaff Rule by Tandem Duplications

“…There have been several papers in the past that have verified this symmetry for different values of k for more than 700 different species [1] [2] [12] [16] [17]. Given a genome of length n, the k-limit or the value of k upto which the 2nd Chargaff rule holds was empirically observed to be about 0.7 ln n [19].…”