The exceptional genomic word symmetry along DNA sequences.

BMC Bioinformatics 2016 Feb 3;17:59. Epub 2016 Feb 3.

Department of Medical Sciences and Institute of Biomedicine - iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal, Campus Universitário de Santiago, Aveiro, Portugal.

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.

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12859-016-0905-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4738807PMC
February 2016
5 Reads
2.580 Impact Factor

Publication Analysis

Top Keywords

exceptional symmetry
32
parity rule
12
local exceptional
12
symmetry
11
exceptional
10
genome sequences
8
exceptional genomic
8
genomic word
8
dna sequences
8
word symmetry
8
word groups
8
sequences
5
word
5
propose sliding
4
symmetry genome
4
sequences propose
4
method extract
4
explore exceptional
4
extract values
4
groupconclusions conclude
4

References

(Supplied by CrossRef)

E Chargaff et al.
Experientia 1950

JD Karkas et al.
Proc Nat Acad Sci USA 1968

DR Forsdyke et al.
2011

D Qi et al.
Bioinformatics 2001

SG Kong et al.
PLoS ONE 2009

SH Zhang et al.
Bioinformatics 2010

DR Forsdyke et al.
Appl Bioinformatics 2004

PF Baisnée et al.
Bioinformatics 2002

G Albrecht-Buehler et al.
Genomics 2007

Similar Publications