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Gapped Pattern Statistics

Philippe Duchon, Cyril Nicaud, Carine Pivoteau, Marc Herbstritt
2017 Annual Symposium on Combinatorial Pattern Matching  
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

Jeff Elhai
2001 Journal of Computational Biology  
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

Samuel Karlin, Chris Burge, Allan M. Campbell
1992 Nucleic Acids Research  
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

S. Caburet
2005 Genome Research  
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

S. Karlin
1986 Proceedings of the National Academy of Sciences of the United States of America  
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

Ho-Su Sin, Eitetsu Koh, Dae-Soo Kim, Miho Murayama, Kazuhiro Sugimoto, Yuji Maeda, Atsumi Yoshida, Mikio Namiki
2010 Journal of Human Genetics  
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

Paul D. W. Kirk, Maxime Huvet, Anat Melamed, Goedele N. Maertens, Charles R. M. Bangham
2016 Nature Microbiology  
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]

E. Levy, A. Barak, A. Fisher, E. Akkermans
2016 arXiv   pre-print
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

C. Morfonios, P. Schmelcher, P. A. Kalozoumis, F. K. Diakonos
2014 Nonlinear dynamics  
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]

Shintaro Narisada, Diptarama Hendrian, Kazuyuki Narisawa, Shunsuke Inenaga, Ayumi Shinohara
2019 arXiv   pre-print
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]

Paul D. W. Kirk, Maxime Huvet, Anat Melamed, Goedele N. Maertens, Charles R. M. Bangham
2015 bioRxiv   pre-print
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]

François Le Gall, Saeed Seddighin
2020 arXiv   pre-print
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

Tatsuhiko TSUNODA, Masao FUKAGAWA, Toshihisa TAKAGI
1998 Biocomputing '99  
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

Amanda Malvessi Cattani, Franciele Maboni Siqueira, Rafael Lucas Muniz Guedes, Irene Silveira Schrank, Mitchell F. Balish
2016 PLoS ONE  
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

Vincent Colot, Vicki Haedens, Jean-Luc Rossignol
1998 Molecular and Cellular Biology  
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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