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Correlation of folding energies of fragments of genomic sequences with their symmetry indexes

Correlation of folding energies of fragments of genomic sequ...

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者： Lei Wang Han-Qi Yang Shang-Hong Zhang Key Laboratory of Gene Engineering of Ministry of Education and Biotechnology Research CenterSun Yat-sen University

Background:Strand symmetry,a ubiquitous phenomenon existing in all cellular genomes studied,is the marked similarity of the frequencies of oligonucleotides to those of their respective reverse complements within single strands of sufficiently long genomic *** is one of the major causes for the existence of two common profiles for genomic oligonucleotide frequencies(Zhang and Wang,Genomics 2011,97:330-331).However,the riddle of strand symmetry is far from being *** of the hypotheses for its origin is the selection of stem-loop structures in single-stranded genomic *** our previous work has indicated that stem-loop potential of single-stranded genomic DNA would contribute little to strand symmetry for higher-order oligonucleotides(Zhang and Huang,Bioinformatics 2010,26:478-485),its contribution to lower-order strand symmetry is not clear. Methods:We analyzed 90 representative prokaryotic genomes(including archaea and bacteria and with a wide range of GC content).Fragments of genomic sequences were obtained by a sliding window of various lengths(200 bp,500 bp,1000 bp and 5000 bp, respectively).We evaluated the stem-loop potential of fragments of genomic sequences in terms of folding energies(dG in kcal/mol) and calculated the symmetry indexes of the corresponding fragments for correlation analysis. Results:There is not an overall correlation pattern for the folding energies and symmetry *** coefficients of correlation may be positive or negative,and may be significant or *** addition,while symmetry indexes increase with the lengths of fragments of genomic sequences,their correlations with the corresponding folding energies usually decrease,especially for lower-order *** of the correlation analysis are in contradiction with the assumption of the stem-loop hypothesis. Conclusions:The contribution of local stem-loop potential of single-stranded genomic DNA to the formation and maintenance of strand symme

关键词： strand symmetry stem-loop potential folding energy genomic sequence

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