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The collapse of the periodicity sequence in the stable range  [PDF]
Birgit Richter
Mathematics , 2006,
Abstract: The stabilization of Hochschild homology of commutative algebras is Gamma homology. We describe a cyclic variant of Gamma homology and prove that the associated analogue of Connes' periodicity sequence becomes almost trivial, because the cyclic version coincides with the ordinary version from homological degree two on. We offer an alternative explanation for this by proving that the B-operator followed by the stabilization map is trivial from degree one on.
Sequence periodicity of Escherichia coli is concentrated in intergenic regions
Sergey Hosid, Edward N Trifonov, Alexander Bolshoy
BMC Molecular Biology , 2004, DOI: 10.1186/1471-2199-5-14
Abstract: Here we demonstrate that practically only ApA/TpT dinucleotides contribute to overall dinucleotide periodicity in Escherichia coli. The noncoding sequences reveal this periodicity much more prominently compared to protein-coding sequences. The sequence periodicity of ApC/GpT, ApT and GpC dinucleotides along the Escherichia coli K-12 is found to be located as well mainly within the intergenic regions.The observed concentration of the dinucleotide sequence periodicity in the intergenic regions of E. coli suggests that the periodicity is a typical property of prokaryotic intergenic regions. We suppose that this preferential distribution of dinucleotide periodicity serves many biological functions; first of all, the regulation of transcription.DNA sequence periodicity with the period about 10–11 base pairs (bp) has been long known in eukaryotic DNA sequences. It was discovered recently in prokaryotic sequences as well [1-6]. The periodicity in Eubacteria sequences usually shows the period close to 11 bp [1]. This period is clearly different from the structural helical period of 10.5–10.6 bp/turn [7,8]. The difference was interpreted [1,2] as a possible reflection of the sequence dependent writhe of prokaryotic DNA. In the work [9] it was demonstrated that the periodicity in the bacterial genomes, in E. coli as well, is distributed in a non-uniform way, in scattered segments of the size 100–150 bases. It was also known for a long time that quite a few DNA promoter regions of E. coli possess the sequence periodicity of AA and TT dinucleotides [10].The sequence periodicity of AA/TT dinucleotides is frequently associated with sequence-dependent DNA curvature, which is known to play an important role in the initiation of transcription of many genes (for reviews, see [11-15]). Using different models and approaches for prediction of intrinsic DNA curvature it was shown that many E. coli promoters have upstream curved sequences [16,17]. Pedersen et al. [18] showed that promoter
Periodicity, repetitions, and orbits of an automatic sequence  [PDF]
Jean-Paul Allouche,Narad Rampersad,Jeffrey Shallit
Computer Science , 2008,
Abstract: We revisit a technique of S. Lehr on automata and use it to prove old and new results in a simple way. We give a very simple proof of the 1986 theorem of Honkala that it is decidable whether a given k-automatic sequence is ultimately periodic. We prove that it is decidable whether a given k-automatic sequence is overlap-free (or squareefree, or cubefree, etc.) We prove that the lexicographically least sequence in the orbit closure of a k-automatic sequence is k-automatic, and use this last result to show that several related quantities, such as the critical exponent, irrationality measure, and recurrence quotient for Sturmian words with slope alpha, have automatic continued fraction expansions if alpha does.
Genomic Sequence around Butterfly Wing Development Genes: Annotation and Comparative Analysis  [PDF]
Inês C. Concei??o, Anthony D. Long, Jonathan D. Gruber, Patrícia Beldade
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0023778
Abstract: Background Analysis of genomic sequence allows characterization of genome content and organization, and access beyond gene-coding regions for identification of functional elements. BAC libraries, where relatively large genomic regions are made readily available, are especially useful for species without a fully sequenced genome and can increase genomic coverage of phylogenetic and biological diversity. For example, no butterfly genome is yet available despite the unique genetic and biological properties of this group, such as diversified wing color patterns. The evolution and development of these patterns is being studied in a few target species, including Bicyclus anynana, where a whole-genome BAC library allows targeted access to large genomic regions. Methodology/Principal Findings We characterize ~1.3 Mb of genomic sequence around 11 selected genes expressed in B. anynana developing wings. Extensive manual curation of in silico predictions, also making use of a large dataset of expressed genes for this species, identified repetitive elements and protein coding sequence, and highlighted an expansion of Alcohol dehydrogenase genes. Comparative analysis with orthologous regions of the lepidopteran reference genome allowed assessment of conservation of fine-scale synteny (with detection of new inversions and translocations) and of DNA sequence (with detection of high levels of conservation of non-coding regions around some, but not all, developmental genes). Conclusions The general properties and organization of the available B. anynana genomic sequence are similar to the lepidopteran reference, despite the more than 140 MY divergence. Our results lay the groundwork for further studies of new interesting findings in relation to both coding and non-coding sequence: 1) the Alcohol dehydrogenase expansion with higher similarity between the five tandemly-repeated B. anynana paralogs than with the corresponding B. mori orthologs, and 2) the high conservation of non-coding sequence around the genes wingless and Ecdysone receptor, both involved in multiple developmental processes including wing pattern formation.
Genomic Networks of Hybrid Sterility  [PDF]
Leslie M. Turner ,Michael A. White,Diethard Tautz,Bret A. Payseur
PLOS Genetics , 2014, DOI: doi/10.1371/journal.pgen.1004162
Abstract: Hybrid dysfunction, a common feature of reproductive barriers between species, is often caused by negative epistasis between loci (“Dobzhansky-Muller incompatibilities”). The nature and complexity of hybrid incompatibilities remain poorly understood because identifying interacting loci that affect complex phenotypes is difficult. With subspecies in the early stages of speciation, an array of genetic tools, and detailed knowledge of reproductive biology, house mice (Mus musculus) provide a model system for dissecting hybrid incompatibilities. Male hybrids between M. musculus subspecies often show reduced fertility. Previous studies identified loci and several X chromosome-autosome interactions that contribute to sterility. To characterize the genetic basis of hybrid sterility in detail, we used a systems genetics approach, integrating mapping of gene expression traits with sterility phenotypes and QTL. We measured genome-wide testis expression in 305 male F2s from a cross between wild-derived inbred strains of M. musculus musculus and M. m. domesticus. We identified several thousand cis- and trans-acting QTL contributing to expression variation (eQTL). Many trans eQTL cluster into eleven ‘hotspots,’ seven of which co-localize with QTL for sterility phenotypes identified in the cross. The number and clustering of trans eQTL—but not cis eQTL—were substantially lower when mapping was restricted to a ‘fertile’ subset of mice, providing evidence that trans eQTL hotspots are related to sterility. Functional annotation of transcripts with eQTL provides insights into the biological processes disrupted by sterility loci and guides prioritization of candidate genes. Using a conditional mapping approach, we identified eQTL dependent on interactions between loci, revealing a complex system of epistasis. Our results illuminate established patterns, including the role of the X chromosome in hybrid sterility. The integrated mapping approach we employed is applicable in a broad range of organisms and we advocate for widespread adoption of a network-centered approach in speciation genetics.
Automatic Seed Generation Using Discrete Cosine Transform for 2D Region Growing Segmentation of Computed Tomography Image Sequence - A New Hybrid Segmentation Technique  [PDF]
C.G. Ravichandran,G. Ravindran
Journal of Applied Sciences , 2007,
Abstract: This research proposes and implements a novel approach that integrates region and edge information for segmenting 2D Computed Tomography Image sequence. Subsequent to operation by Gaussian Filter and Edge Detection, the seed value is then calculated by transforming the image from spatial domain to frequency domain. The region is then grown from the seed value by appending each pixel into its region at successive iterations. The speed is increased by parallel region growing process. This approach is fully automatic and does not need manual intervention. The segmented image sequence finds further use in reconstructing a 3D model.
Hidden Periodicity and Chaos in the Sequence of Prime Numbers  [PDF]
A. Bershadskii
Advances in Mathematical Physics , 2011, DOI: 10.1155/2011/519178
Abstract: Logarithmic gaps have been used in order to find a periodic component of the sequence of prime numbers, hidden by a random noise (stochastic or chaotic). It is shown that multiplicative nature of the noise is the main reason for the successful application of the logarithmic gaps transforming the multiplicative noise into an additive one. A relation of this phenomenon to spontaneous neuron activity and to chaotic brain computations has been discussed. 1. Introduction The prime number distribution is apparently random. The apparent randomness can be stochastic or chaotic (deterministic). It is well known that the Riemann zeros obey the chaotic GUE statistics (if the primes are interpreted as the classical periodic orbits of a chaotic system, see for a recent review [1]), whereas the primes themselves are believed to be stochastically distributed (Poissonian-like, etc., [2]). However, recent investigations suggest that primes themselves “ could be eigenvalues of a quantum system whose classical counterpart is chaotic at low energies but increasingly regular at higher energies.” [3]. Therefore, the problem of chaotic (deterministic) behavior of the moderate and small prime numbers is still open. Moreover, there is also an indication of periodic patterns in the prime numbers distribution [3–7]. These patterns, however, have been observed in probability distribution of the gaps between neighboring primes and not in the prime numbers sequence itself (see also [8]). The intrinsic randomness (stochastic or chaotic) of the primes distribution makes the problem of finding the periodic patterns in the prime numbers themselves (if they exist after all) a very difficult one. A physicists may ask: why should one be interested in finding these patterns? The answer is: comparison. If one can recognize patterns in an apparently random system, then one can compare these patterns with the patterns known for some other system of interest. We have already mentioned the comparison with certain quantum systems. Another intrinsic comparison can be made with the computational properties of brains, where the natural numbers certainly should play a crucial role. The neuron signals are also apparently random. Can one compare patterns observed in these signals with the patterns in the prime numbers sequence in a constructive way, in order to shed a light on the computational apparatus of the brains? 2. Logarithmic Gaps It is believed that properties of the gaps between consecutive primes can provide a lot of information about the primes distribution in the natural sequence. The
Stereo Matching Algorithm based on Aligning Genomic Sequence  [PDF]
S. Yu,D. Yan,Y. Dong,H. Tian
Information Technology Journal , 2011,
Abstract: Presently, stereo matching algorithms are almost in purpose of pursuing high matching precision, the whole time spent in algorithms are too long. In this study, we proposed a stereo matching algorithm based on aligning genomic sequence, according to the comparability on the theory of aligning genomic sequences and stereo matching algorithm. Firstly, pixels in each epipolar on stereo image were transformed into the form of genomic sequences and then used calculation method of getting score matrix by comparison of genomic sequence to establish two-dimensional disparity space images. At last, we finally get disparity using searching optimization strategy in aligning genomic sequences to do global optimization. The experimental results show that the whole time of this method is greatly reduced and matching quality is still good.
Differences in DNA curvature-related sequence periodicity between prokaryotic chromosomes and phages, and relationship to chromosomal prophage content
Jacob Abel, Jan Mrazek
BMC Genomics , 2012, DOI: 10.1186/1471-2164-13-188
Abstract: We developed measures of intensity and persistency of DNA curvature-related sequence periodicity and applied them to prokaryotic chromosomes and phages. The results indicate that strong periodic signals present in chromosomes are generally absent in phage genomes. Moreover, chromosomes containing prophages are less likely to possess a persistent periodic signal than chromosomes with no prophages.Absence of DNA curvature-related sequence periodicity in phages could arise from constraints associated with DNA packaging in the viral capsid. Lack of prophages in chromosomes with persistent periodic signal suggests that the sequence periodicity and concomitant DNA curvature could play a role in protecting the chromosomes from integration of phage DNA.
PerPlot & PerScan: tools for analysis of DNA curvature-related periodicity in genomic nucleotide sequences
Jan Mrázek, Tejas Chaudhari, Aryabrata Basu
Microbial Informatics and Experimentation , 2011, DOI: 10.1186/2042-5783-1-13
Abstract: We present novel tools suitable for assessments of DNA curvature-related sequence periodicity in nucleotide sequences at the genome scale. Utility of the present software is demonstrated on a comparison of sequence periodicities in the genomes of Haemophilus influenzae, Methanocaldococcus jannaschii, Saccharomyces cerevisiae, and Arabidopsis thaliana. The software can be accessed through a web interface and the programs are also available for download.The present software is suitable for comparing DNA curvature-related sequence periodicity among different genomes as well as for analysis of intrachromosomal heterogeneity of the sequence periodicity. It provides a quick and convenient way to detect anomalous regions of chromosomes that could have unusual structural and functional properties and/or distinct evolutionary history.Most naturally occurring DNA sequences feature two strong periodic patterns. The first relates to a 3 bp period resulting from amino acid and codon usage biases in protein coding genes. The second arises from periodic spacing of A-tracts (short runs of A or T) phased with the DNA helical period of ~10.5 bp. The periodically spaced A-tracts are a primary indicator of intrinsically bent DNA and the main component of nucleosome positioning signals in eukaryotes [1-3]. Similar periodic patterns are present in prokaryotes, where they could contribute to DNA packaging in the nucleoid [4,5], promote the appropriate mode of supercoiling [6,7], and/or facilitate the initiation and termination of transcription [8,9]. There are significant differences in the character and intensity of these periodic patterns among different genomes as well as among different segments of the same genome [4,6,7,10]. In some species, the intragenomic heterogeneity of the sequence periodicity has been linked to local variance in gene expression and chromatin structure [4,11,12].Despite the biological significance of DNA curvature-related sequence periodicity, there are virtual
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