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Gapped Pattern Statistics
2017
Annual Symposium on Combinatorial Pattern Matching
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More precisely, we study the expected number of maximal α-gapped patterns, as well as the expected length of the longest α-gapped pattern in a random word. ...
We give a probabilistic analysis of parameters related to α-gapped repeats and palindromes in random words, under both uniform and memoryless distributions (where letters have different probabilities, ...
, the expected number of distinct palindromic factors [15] , etc. ...
doi:10.4230/lipics.cpm.2017.21
dblp:conf/cpm/DuchonNP17
fatcat:xafyyxh6z5c35ptdxpjnqmdxyy
Determination of Bias in the Relative Abundance of Oligonucleotides in DNA Sequences
2001
Journal of Computational Biology
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In fact, the efficacy of statistics based on Markov analysis even at the highest order were inferior in predicting actual frequencies of oligonucleotides to methods that factored out biases of internal ...
The expected frequency of an oligonucleotide calculated from a maximal order Markov model was shown to be a degenerate case of the expected frequency calculated from biases of all subwords, arising when ...
ACKNOWLEDGEMENTS I would like to thank Misha Gelfand, KT Young, and an anonymous reviewer for valuable comments and suggestions and Kathy Hoke for advice on statistical matters. ...
doi:10.1089/106652701300312922
pmid:11454303
fatcat:6gjdazce35c6xm3jahnpvbl6vu
Statistical analyses of counts and distributions of restriction sites in DNA sequences
1992
Nucleic Acids Research
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Both 4-and 6-bp average palindrome counts were significantly low in all bacteriophages except one, probably as a means of avoiding restriction enzyme cleavage. ...
The exception, T4 of normal 4-and 6-palindrome counts, putatively derives protection from modification of cytosine to hydroxymethylcytosine plus glycosylation. ...
Given expected counts of palindromes based on mono-, di-, or trinucleotide frequencies, the correlation statistics of the expectations with the observed counts are determined by the calculations of Eq. ...
doi:10.1093/nar/20.6.1363
pmid:1313968
pmcid:PMC312184
fatcat:hj5apuhyhjggxmwcvliqji7q4a
Human ribosomal RNA gene arrays display a broad range of palindromic structures
2005
Genome Research
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In cells from individuals with a deficiency in the WRN RecQ helicase (Werner syndrome), the proportion of palindromes increased to one-half. ...
While we confirmed this arrangement in many cases, unorthodox patterns were also observed in normal individuals, with one-third of the rDNA units rearranged to form apparently palindromic structures (noncanonical ...
Weitzman for helpful comments on the manuscript. This work was supported by grants from the NIH, the AFM, and the ARC. S.C. was supported by a Ph.D. fellowship from ARC. ...
doi:10.1101/gr.3970105
pmid:16024823
pmcid:PMC1182220
fatcat:qcswq2zohnfcjczm5aihjnien4
Significant potential secondary structures in the Epstein-Barr virus genome
1986
Proceedings of the National Academy of Sciences of the United States of America
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The distribution of long dyad symmetry pairings emphasizes two regions, the 5' third of the 3.1-kilobase-pair (kbp) repeat and the oriP region, the latter essential for Epstein-Barr virus replication during ...
A 600-base-pair (bp) stretch in the 3.1-kbp repeat can establish an extended hairpin loop of stem length in excess of 208 bp of predominantly G+C stacking. Moreover, the 3. ...
The number of distinct dyad pairings concentrated in this region is great. ...
doi:10.1073/pnas.83.18.6915
pmid:3018750
pmcid:PMC386621
fatcat:l2qecjqlozhxpbxun2wob6ew44
Human endogenous retrovirus K14C drove genomic diversification of the Y chromosome during primate evolution
2010
Journal of Human Genetics
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Based on our phylogenetic analysis of the solitary LTRs derived from HERV-K14C on the Y chromosome we suggested that these sequences were generated as pairs of identical sequences. ...
Interestingly, 29 of all 146 copies were located in Y chromosome, and these 29 copies were mostly dispersed in the palindromic region. ...
The authors also thank Ms. E. Saitoh and Ms. N. Kanno for technical assistance. ...
doi:10.1038/jhg.2010.94
pmid:20703239
fatcat:7q3gugvqg5fxpam4lp7bduamle
Retroviruses integrate into a shared, non-palindromic DNA motif
2016
Nature Microbiology
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Strand transfer 38 results in single-stranded DNA gaps that are filled in and repaired by host cellular enzymes. 39 Depending on the retrovirus, the strand transfer reaction takes place with a 4 (e.g. ...
HTLV-1 and 2) base pair stagger, giving 41 rise to a duplication of the respective number of nucleotides at the integration site. 42 43 44 Integration is not random: each retrovirus has characteristic ...
The API is 1 if the sequence is perfectly 85 palindromic, 0 if the sequence is as palindromic as expected by chance, and negative if the 86 sequence is less palindromic than expected by chance. ...
doi:10.1038/nmicrobiol.2016.212
pmid:27841853
fatcat:fvvbgy6oivdpfo6aaffpcwybeu
Topological properties of Fibonacci quasicrystals : A scattering analysis of Chern numbers
[article]
2016
arXiv
pre-print
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We report on a study of topological properties of Fibonacci quasicrystals. Chern numbers which label the dense set of spectral gaps, are shown to be related to the underlying palindromic symmetry. ...
Conveniently designed gap modes with spectral properties directly related to the Chern numbers allow to scan these phases. An effective topological Fabry-Perot cavity is presented. ...
This periodic occurrence of palindromic chains, as we shall see, is underlying the existence of Chern numbers in the gap labeling relation (1). ...
arXiv:1509.04028v3
fatcat:mprrtcl4sbdvvmpcwnvzx6kf3e
Local symmetry dynamics in one-dimensional aperiodic lattices: a numerical study
2014
Nonlinear dynamics
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A unifying description of lattice potentials generated by aperiodic one-dimensional sequences is proposed in terms of their local reflection or parity symmetry properties. ...
A striking aspect of such a property is given by the return maps of sequential spacings of local symmetry axes, which typically traverse few-point symmetry orbits. ...
Further financial support by the Greek Scholarship Foundation IKY in the framework of an exchange program with Germany (IKYDA) is also acknowledged. ...
doi:10.1007/s11071-014-1422-1
fatcat:dxoks7nzhrcujisbtmzlh2hcuy
Efficient computation of longest single-arm-gapped palindromes in a string
[article]
2019
arXiv
pre-print
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In this paper, we introduce new types of approximate palindromes called single-arm-gapped palindromes (shortly SAGPs). ...
Here we call wu and u^R w^R the arm of the SAGP, and |uv| the length of the arm. We classify SAGPs into two groups: those which have ucu^R as a maximal palindrome (type-1), and the others (type-2). ...
The research of Shunsuke Inenaga is in part supported by JSPS KAKENHI Grant Numbers 26280003 and 17H01697. ...
arXiv:1609.03000v4
fatcat:bbfy65m7sbbtlfx3acutzlsuiq
Retroviruses integrate into a shared, non-palindromic motif
[article]
2015
bioRxiv
pre-print
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nucleotide motif that occurs in approximately equal proportions on the plus-strand and the minus-strand of the host genome. ...
The results show that the palindromic consensus sequence is not present in individual integration sites, but appears to arise in the population average as a consequence of the existence of a non-palindromic ...
ACKNOWLEDGEMENTS The authors wish to thank the following individuals for providing materials: Alexander Zhyvoloup and Ariberto Fassati, Division of Infection and Immunity, University College London; and ...
doi:10.1101/034991
fatcat:iryw326uwjc2vhxzqaxicxiqnu
Quantum Meets Fine-grained Complexity: Sublinear Time Quantum Algorithms for String Problems
[article]
2020
arXiv
pre-print
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Our results shed light on a very surprising fact: Although the classic solutions for LCS and LPS are almost identical (via suffix trees), their quantum computational complexities are different. ...
Longest common substring (LCS), longest palindrome substring (LPS), and Ulam distance (UL) are three fundamental string problems that can be classically solved in near linear time. ...
Acknowledgments The authors are grateful to Michael Saks and C. Seshadhri for helpful correspondence. FLG was supported by the JSPS KAKENHI grants Nos. ...
arXiv:2010.12122v1
fatcat:cmh6vb2tlnatzjkc232dulk6ry
Time and Memory Efficient Algorithm for Extracting Palindromic and Repetitive Subsequences in Nucleic Acid Sequences
1998
Biocomputing '99
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Especially, it is desirable to extract the same character sequences of arbitrary length (especially, very long ones) which co-occur at an arbitrary separation. ...
Also, the genetic network, transduction pathway, and tissue specicity largely depend on these. ...
Acknowledgements This work is partially supported by Grant-in-Aid for Scientic Research on Priority Areas, \Genome Science" from the Ministry of Education, Science, Sports, and Culture, Japan. ...
doi:10.1142/9789814447300_0020
fatcat:74wsnnzbhrdm3e2b5abf745yqa
Repetitive Elements in Mycoplasma hyopneumoniae Transcriptional Regulation
2016
PLoS ONE
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Computational analysis demonstrated the presence of 144 tandem repeats and 1,171 palindromic elements. ...
revealed differential expression among genes showing variable numbers of repetitive elements. ...
The adhesin-coding genes are important virulence factors and seem to be regulated depending on the presence or absence of palindromic repeats. ...
doi:10.1371/journal.pone.0168626
pmid:28005945
pmcid:PMC5179023
fatcat:4ialoibnanbcld3qy2ye3zyczi
Extensive, Nonrandom Diversity of Excision Footprints Generated byDs-Like TransposonAscot-1Suggests New Parallels with V(D)J Recombination
1998
Molecular and Cellular Biology
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An evaluation of the contribution of small palindromic nucleotide additions produced by transposon excision to the spectrum of spontaneous mutations is also presented. ...
Factors likely to be involved in these biases suggest new parallels between the excision reaction performed by transposons of thehATfamily and V(D)J recombination. ...
Special thanks are due to Michael Ronemus for critical reading of the manuscript. ...
doi:10.1128/mcb.18.7.4337
pmid:9632817
pmcid:PMC109017
fatcat:w72rwhyumnh3zn4x7bzt2slyqa
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