Evaluation of the Persistence of Higher-Order Strand Symmetry in Genomic Sequences by Novel Word Symmetry Distance Analysis
For the ubiquitous phenomenon of strand symmetry, it has been shown that it may persist for higher-order oligonucleotides. However, there is no consensus about to what extent (order of oligonucleotides or length of words) strand symmetry still persists. To determine the extent of strand symmetry in...
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doaj-ef0a36b8a6d04e609e0fc7b4e089195b2020-11-25T00:26:50ZengFrontiers Media S.A.Frontiers in Genetics1664-80212019-03-011010.3389/fgene.2019.00148435739Evaluation of the Persistence of Higher-Order Strand Symmetry in Genomic Sequences by Novel Word Symmetry Distance AnalysisBi HuangLi-Fang HuangShang-Hong ZhangFor the ubiquitous phenomenon of strand symmetry, it has been shown that it may persist for higher-order oligonucleotides. However, there is no consensus about to what extent (order of oligonucleotides or length of words) strand symmetry still persists. To determine the extent of strand symmetry in genomic sequences is critically important for the further understanding of the phenomenon. Based on previous studies, we have developed an algorithm for the novel word symmetry distance analysis. We applied it to evaluate the higher-order strand symmetry for 206 archaeal genomes and 2,659 bacterial genomes. Our results show that the new approach could provide a clear-cut criterion to determine the extent of strand symmetry for a group of genomes or individual genomes. According to the new measure, strand symmetry would tend to persist for up to 8-mers in archaeal genomes, and up to 9-mers in bacterial genomes. And the persistence may vary from 6- to 9-mers in individual genomes. Moreover, higher-order strand symmetry would tend to positively correlate with GC content and mononucleotide symmetry levels of genomic sequences. The variations of higher-order strand symmetry among genomes would indicate that strand symmetry itself may not be strictly relevant to biological functions, which would provide some insights into the origin and evolution of the phenomenon.https://www.frontiersin.org/article/10.3389/fgene.2019.00148/fullthe second parity rulehigher-order oligonucleotidewhole-genome sequencesfrequency analysisword symmetry distance (WSD) |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Bi Huang Li-Fang Huang Shang-Hong Zhang |
spellingShingle |
Bi Huang Li-Fang Huang Shang-Hong Zhang Evaluation of the Persistence of Higher-Order Strand Symmetry in Genomic Sequences by Novel Word Symmetry Distance Analysis Frontiers in Genetics the second parity rule higher-order oligonucleotide whole-genome sequences frequency analysis word symmetry distance (WSD) |
author_facet |
Bi Huang Li-Fang Huang Shang-Hong Zhang |
author_sort |
Bi Huang |
title |
Evaluation of the Persistence of Higher-Order Strand Symmetry in Genomic Sequences by Novel Word Symmetry Distance Analysis |
title_short |
Evaluation of the Persistence of Higher-Order Strand Symmetry in Genomic Sequences by Novel Word Symmetry Distance Analysis |
title_full |
Evaluation of the Persistence of Higher-Order Strand Symmetry in Genomic Sequences by Novel Word Symmetry Distance Analysis |
title_fullStr |
Evaluation of the Persistence of Higher-Order Strand Symmetry in Genomic Sequences by Novel Word Symmetry Distance Analysis |
title_full_unstemmed |
Evaluation of the Persistence of Higher-Order Strand Symmetry in Genomic Sequences by Novel Word Symmetry Distance Analysis |
title_sort |
evaluation of the persistence of higher-order strand symmetry in genomic sequences by novel word symmetry distance analysis |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Genetics |
issn |
1664-8021 |
publishDate |
2019-03-01 |
description |
For the ubiquitous phenomenon of strand symmetry, it has been shown that it may persist for higher-order oligonucleotides. However, there is no consensus about to what extent (order of oligonucleotides or length of words) strand symmetry still persists. To determine the extent of strand symmetry in genomic sequences is critically important for the further understanding of the phenomenon. Based on previous studies, we have developed an algorithm for the novel word symmetry distance analysis. We applied it to evaluate the higher-order strand symmetry for 206 archaeal genomes and 2,659 bacterial genomes. Our results show that the new approach could provide a clear-cut criterion to determine the extent of strand symmetry for a group of genomes or individual genomes. According to the new measure, strand symmetry would tend to persist for up to 8-mers in archaeal genomes, and up to 9-mers in bacterial genomes. And the persistence may vary from 6- to 9-mers in individual genomes. Moreover, higher-order strand symmetry would tend to positively correlate with GC content and mononucleotide symmetry levels of genomic sequences. The variations of higher-order strand symmetry among genomes would indicate that strand symmetry itself may not be strictly relevant to biological functions, which would provide some insights into the origin and evolution of the phenomenon. |
topic |
the second parity rule higher-order oligonucleotide whole-genome sequences frequency analysis word symmetry distance (WSD) |
url |
https://www.frontiersin.org/article/10.3389/fgene.2019.00148/full |
work_keys_str_mv |
AT bihuang evaluationofthepersistenceofhigherorderstrandsymmetryingenomicsequencesbynovelwordsymmetrydistanceanalysis AT lifanghuang evaluationofthepersistenceofhigherorderstrandsymmetryingenomicsequencesbynovelwordsymmetrydistanceanalysis AT shanghongzhang evaluationofthepersistenceofhigherorderstrandsymmetryingenomicsequencesbynovelwordsymmetrydistanceanalysis |
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