Word Size Research Articles

Local Similarities Approximation in DNA Sequences Based on Pairwise Sequence Aligner Algorithm

Sequence alignment is a way of arranging primary sequences of DNA, RNA, or protein to identify regions of similarity. This region may be a consequence of functional, structural, or evolutionary relationships between the sequences. An algorithm is proposed for finding approximate local similarities in DNA sequences (AFALS-N). This algorithm is capable of finding the similarity between two sequences by generating all the possible words in the first sequence, then finding the exact matches in the second sequence. The selection of the obtained results is essential to reduce the number of possible results that in turn reduces the searching time. Results show that the proposed algorithm has reduced the searching time to an average of 20% in regard to PatternHunter algorithm. The objective of this work was evident by maintaining balance between the execution time and the size of seeds and the sensitivity. Improved execution time with 66% of sensitivity are obtained with the same word size as those used in other algorithms.

Applying Shannon's information theory to bacterial and phage genomes and metagenomes

All sequence data contain inherent information that can be measured by Shannon's uncertainty theory. Such measurement is valuable in evaluating large data sets, such as metagenomic libraries, to prioritize their analysis and annotation, thus saving computational resources. Here, Shannon's index of complete phage and bacterial genomes was examined. The information content of a genome was found to be highly dependent on the genome length, GC content, and sequence word size. In metagenomic sequences, the amount of information correlated with the number of matches found by comparison to sequence databases. A sequence with more information (higher uncertainty) has a higher probability of being significantly similar to other sequences in the database. Measuring uncertainty may be used for rapid screening for sequences with matches in available database, prioritizing computational resources, and indicating which sequences with no known similarities are likely to be important for more detailed analysis.

Deterministic polynomial-time algorithms for designing short DNA words

Designing short DNA words is a problem of constructing a set (i.e., code) of n DNA strings (i.e., words) with the minimum length such that the Hamming distance between each pair of words is at least k and the n words satisfy a set of additional constraints. This problem has applications in, e.g., DNA self-assembly and DNA arrays. Previous works include those that extended results from coding theory to obtain bounds on code and word sizes for biologically motivated constraints and those that applied heuristic local searches, genetic algorithms, and randomized algorithms. In particular, Kao, Sanghi, and Schweller [16] developed polynomial-time randomized algorithms to construct n DNA words of length within a multiplicative constant of the smallest possible word length (e.g., 9⋅max{logn,k}) that satisfy various sets of constraints with high probability. In this paper, we give deterministic polynomial-time algorithms to construct DNA words based on derandomization techniques. Our algorithms can construct n DNA words of shorter length (e.g., 2.1logn+6.28k) and can satisfy the same sets of constraints as the words constructed by the algorithms of Kao et al.. Furthermore, we extend these new algorithms to construct words that satisfy a larger set of constraints for which the algorithms of Kao et al. do not work.

Designing a Bioengine for Detection and Analysis of Base String on an Affected Sequence in High-Concentration Regions

We design an Algorithm for bioengine. As a program are enable optimal alignments searching between two sequences, the host sequence (normal plant) as well as query sequence (virus). Searching for homologues has become a routine operation of biological sequences in 4 × 4 combination with different subsequence (word size). This program takes the advantage of the high degree of homology between such sequences to construct an alignment of the matching regions. There is a main aim which is to detect the overlapping reading frames. This program also enables to find out the highly infected colones selection highest matching region with minimum gap or mismatch zones and unique virus colones matches. This is a small, portable, interactive, front-end program intended to be used to find out the regions of matching between host sequence and query subsequences. All the operations are carried out in fraction of seconds, depending on the required task and on the sequence length.

Biometrics and Biosecurity 2013

Biometrics and Biosecurity 2013

Querying highly similar sequences

In this paper, we present a solution to the extreme similarity sequencing problem. The extreme similarity sequencing problem consists of finding occurrences of a pattern p in a set S(0), S(1), , S(k), of sequences of equal length, where S(i), for all 1≤i≤k, differs from S(0) by a constant number of errors - around 10 in practice. We present an asymptotically fast O(n + occ logocc) time algorithm, as well as a practical O(nk/w) time algorithm for solving this problem, where n is the length of a sequence, occ is the number of candidate occurrences reported by our technique, w is the size of the machine word, and the total number of errors is bounded by k - the number of sequences.

Neuroticism as distancing: Perceptual sources of evidence.

Several theories and self-reported sources of data link individual differences in negative affectivity to avoidance motivation. Chronic avoidance motivation, through repeated practice, may result in a relatively cognitive distance-enhancing dynamic whereby events and stimuli are perceived as further away from the self, even when they are not threatening. Such predictions are novel but follow from cybernetic theories of self-regulation. In 5 studies (total N = 463), relations of this type were investigated. Study 1 presented participants with phrases that were ambiguous and found that trait negative affect predicted phrase interpretation in a distance-enhancing temporal direction. Study 2 replicated this effect across a systematic manipulation of event valence. Study 3 asked individuals to estimate the size of words and found that individuals higher in neuroticism generally perceived words to be smaller than did individuals lower in neuroticism. In Study 4, people high (but not low) in neuroticism perceived words to be shrinking faster than they were growing. In Study 5, greater perceptual distancing, in a font size estimation task, predicted more adverse reactions to negative events in daily life. Although normative effects varied across studies, consistent support for a chronic distancing perspective of individual differences in negative affectivity was found.

ASP: Automated symbolic computation of approximate symmetries of differential equations

A recent paper (Pakdemirli et al. (2004) [12]) compared three methods of determining approximate symmetries of differential equations. Two of these methods are well known and involve either a perturbation of the classical Lie symmetry generator of the differential system (Baikov, Gazizov and Ibragimov (1988) [7], Ibragimov (1996) [6]) or a perturbation of the dependent variable/s and subsequent determination of the classical Lie point symmetries of the resulting coupled system (Fushchych and Shtelen (1989) [11]), both up to a specified order in the perturbation parameter. The third method, proposed by Pakdemirli, Yürüsoy and Dolapçi (2004) [12], simplifies the calculations required by Fushchych and Shtelen’s method through the assignment of arbitrary functions to the non-linear components prior to computing symmetries. All three methods have been implemented in the new MAPLE package ASP (Automated Symmetry Package) which is an add-on to the MAPLE symmetry package DESOLVII (Vu, Jefferson and Carminati (2012) [25]). To our knowledge, this is the first computer package to automate all three methods of determining approximate symmetries for differential systems. Extensions to the theory have also been suggested for the third method and which generalise the first method to systems of differential equations. Finally, a number of approximate symmetries and corresponding solutions are compared with results in the literature. Program summaryProgram title: ASPCatalogue identifier: AEOG_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEOG_v1_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 15819No. of bytes in distributed program, including test data, etc.: 185052Distribution format: tar.gzProgramming language: MAPLE internal language.Computer: PCs and workstations.Operating system: Linux, Windows XP and Windows 7.RAM: Depends on the type of problem and the complexity of the system (small ≈ MB, large ≈ GB)Word size: Supports 32 and 64 bit platformsClassification: 4.3, 5.Nature of problem:Calculates approximate symmetries for differential equations using any of the three methods as proposed by Baikov, Gazizov and Ibragimov [1,2], Fushchych and Shtelen [3] or Pakdemirli, Yürüsoy and Dolapci [4]. Package includes an altered version of the DESOLVII package (Vu, Jefferson and Carminati [5]).Solution method:See Nature of problem above.Restrictions:Sufficient memory may be required for large systems.Running time:Depends on the type of problem and the complexity of the system (small ≈ seconds, large ≈ hours).

Multiplier-free DCT approximations for RF multi-beam digital aperture-array space imaging and directional sensing

Multi-beamforming is an important requirement for broadband space imaging applications based on dense aperture arrays (AAs). Usually, the discrete Fourier transform is the transform of choice for AA electromagnetic imaging. Here, the discrete cosine transform (DCT) is proposed as an alternative, enabling the use of emerging fast algorithms that offer greatly reduced complexity in digital arithmetic circuits. We propose two novel high-speed digital architectures for recently proposed fast algorithms (Bouguezel, Ahmad and Swamy 2008 Electron. Lett. 44 1249–50) (BAS-2008) and (Cintra and Bayer 2011 IEEE Signal Process. Lett. 18 579–82) (CB-2011) that provide good approximations to the DCT at zero multiplicative complexity. Further, we propose a novel DCT approximation having zero multiplicative complexity that is shown to be better for multi-beamforming AAs when compared to BAS-2008 and CB-2011. The far-field array pattern of ideal DCT, BAS-2008, CB-2011 and proposed approximation are investigated with error analysis. Extensive hardware realizations, implementation details and performance metrics are provided for synchronous field programmable gate array (FPGA) technology from Xilinx. The resource consumption and speed metrics of BAS-2008, CB-2011 and the proposed approximation are investigated as functions of system word size. The 8-bit versions are mapped to emerging asynchronous FPGAs leading to significantly increased real-time throughput with clock rates at up to 925.6 MHz implying the fastest DCT approximations using reconfigurable logic devices in the literature.

A digital hardware fast algorithm and FPGA-based prototype for a novel 16-point approximate DCT for image compression applications

The discrete cosine transform (DCT) is the key step in many image and video coding standards. The eight-point DCT is an important special case, possessing several low-complexity approximations widely investigated. However, the 16-point DCT transform has energy compaction advantages. In this sense, this paper presents a new 16-point DCT approximation with null multiplicative complexity. The proposed transform matrix is orthogonal and contains only zeros and ones. The proposed transform outperforms the well-known Walsh–Hadamard transform and the current state-of-the-art 16-point approximation. A fast algorithm for the proposed transform is also introduced. This fast algorithm is experimentally validated using hardware implementations that are physically realized and verified on a 40 nm CMOS Xilinx Virtex-6 XC6VLX240T FPGA chip for a maximum clock rate of 342 MHz. Rapid prototypes on FPGA for a 8-bit input word size show significant improvement in compressed image quality by up to 1–2 dB at the cost of only eight adders compared to the state-of-art 16-point DCT approximation algorithm in the literature (Bouguezel et al 2010 Proc. 53rd IEEE Int. Midwest Symp. on Circuits and Systems).

Efficient SIMD solution of multiple systems of stiff IVPs

The parallel solution of multiple systems of initial-value problems (IVPs) in ordinary differential equations is challenging because the amount of computation involved in solving a given IVP is generally not well correlated with that of solving another. In this paper, we describe how to efficiently solve multiple systems of stiff IVPs in parallel within a single-instruction, multiple-data (SIMD) implementation on the Cell Broadband Engine (CBE) of the RODAS solver for stiff IVPs. We solve two systems of stiff IVPs simultaneously on each of the eight synergistic processing elements per CBE chip for a total of 16 systems of IVPs. We demonstrate a speedup of 1.89 (a parallel efficiency of over 94%) over the corresponding serial code on a realistic example involving the operation of a chemical reactor. The techniques described apply to other multi-core processors besides the CBE and can be expected to increase in importance as computer architectures evolve to feature larger word sizes.

Exploiting word-level parallelism for fast convolutions and their applications in approximate string matching

We develop a method for performing convolutions efficiently in a word RAM model of computation, having a word size of w=Ω(logn) bits, where n is the input size. The basic idea is to pack several elements of the input vector into a single computer word, effectively enabling parallel computation of convolutions. The technique is applied to approximate string matching under Hamming distance. The obtained algorithms are the fastest known. In particular, we reduce the complexity of the Amir et al. (2000) algorithm for k-mismatches from O(nklogk) to O(n+nk/wlogk). Those algorithms impose some (not severe) limitation on the pattern length, m. We present another, less efficient however, technique based on word-level parallelism, which works without the pattern length limitation.

State cycles, initialization and the Trivium stream cipher

Trivium is a keystream generator for a binary additive synchronous stream cipher. It was selected in the final portfolio for the Profile 2 category of the eSTREAM project. The keystream generator is constructed using bit-based shift registers. In this paper we present an alternate representation of Trivium using word-based shift registers, with a word size of three bits. This representation is useful for determining cycles of internal state values. Under this representation it is clear that the state space can be partitioned into subspaces and that over some of these subspaces the state update function is effectively linear. The role of the initialization process is critical in ensuring the states used for generating keystream are updated nonlinearly at some point, as the state update function alone does not provide this.

Measuring persistence in a stationary time series using the complex network theory

A growing interest exists currently in the analysis of time series by the complex network theory. Here we present a simple and quick way for mapping time series to complex networks. Using a simple rule allows us to transform time series into a textual sequence then we divide it into words with fixed size. Distinct words are nodes of the network, and we have complete control on the network scale by adjusting the word size. Two nodes are linked if their associated words co-occur in sequence. We show that the network topological measures quantify the persistence and the long range correlations in fractional Brownian processes. For a particular word size we assume some relations between the topological measures and the Hurst exponent which characterised the persistence in fractional Brownian processes.

A BIT-PARALLEL DYNAMIC PROGRAMMING ALGORITHM SUITABLE FOR DNA SEQUENCE ALIGNMENT

Myers' elegant and powerful bit-parallel dynamic programming algorithm for approximate string matching has a restriction that the query length should be within the word size of the computer, typically 64. We propose a modification of Myers' algorithm, in which the modification has a restriction not on the query length but on the maximum number of mismatches (substitutions, insertions, or deletions), which should be less than half of the word size. The time complexity is O(m log |Σ|), where m is the query length and |Σ| is the size of the alphabet Σ. Thus, it is particularly suited for sequences on a small alphabet such as DNA sequences. In particular, it is useful in quickly extending a large number of seed alignments against a reference genome for high-throughput short-read data produced by next-generation DNA sequencers.

A SHORT INTRODUCTION TO SOME RECENT PROGRESS IN PHYLOGENETIC NETWORK RECONSTRUCTION, GENOME MAPPING, GENE EXPRESSION ANALYSIS, MOLECULAR DYNAMIC SIMULATION, AND OTHER PROBLEMS IN BIOINFORMATICS

Journal of Bioinformatics and Computational BiologyVol. 10, No. 04, 1203002 (2012) Free AccessA SHORT INTRODUCTION TO SOME RECENT PROGRESS IN PHYLOGENETIC NETWORK RECONSTRUCTION, GENOME MAPPING, GENE EXPRESSION ANALYSIS, MOLECULAR DYNAMIC SIMULATION, AND OTHER PROBLEMS IN BIOINFORMATICSLIMSOON WONGLIMSOON WONG Search for more papers by this author https://doi.org/10.1142/S0219720012030023Cited by:1 Next AboutSectionsPDF/EPUB ToolsAdd to favoritesDownload CitationsTrack CitationsRecommend to Library ShareShare onFacebookTwitterLinked InRedditEmail References Y.-J. Heet al., J. Bioinform. Comput. Biol. 4(1), 59 (2006). Link, Google ScholarL. van Iersel, S. Kelk and M. Mnich, J. Bioinform. Comput. Biol. 7(4), 597 (2009). Link, Google ScholarP. Gambette, B. Berry and C. Paul, J. Bioinform. Comput. Biol. 10(4), 1250004 (2012). Link, Google ScholarR. Pokrzywa, J. Bioinform. Comput. Biol. 6(2), 403 (2008). Link, Google ScholarK. Kimura, A. Koike and K. Nakai, J. Bioinform. Comput. Biol. 10(4), 1250002 (2012). Link, Google ScholarL. Licamele and L. Getoor, J. Bioinform. Comput. Biol. 9(3), 431 (2011). Link, Google ScholarO. Obidat and C. K. Reddy, J. Bioinform. Comput. Biol. 10(1), 1240002 (2012). Medline, Google ScholarV. Olmanet al., J. Bioinform. Comput. Biol. 4(5), 999 (2006). Link, Google ScholarQ. Han and G. Dong, J. Bioinform. Comput. Biol. 10(4), 1250005 (2012). Link, Google ScholarJ. Xu, J. Bioinform. Comput. Biol. 10(4), 1250007 (2012). Link, Google ScholarR. Kanagasabaiet al., J. Bioinform. Comput. Biol. 5(6), 1319 (2007). Link, Google ScholarC. H. Kohet al., J. Bioinform. Comput. Biol. 7(6), 973 (2009). Link, Google ScholarB. Limayeet al., J. Bioinform. Comput. Biol. 10(4), 1250006 (2012). Link, Google ScholarA. A. Terentievet al., J. Bioinform. Comput. Biol. 10(2), 1241012 (2012). Link, Google ScholarS. Hwanget al., J. Bioinform. Comput. Biol. 9(), 15 (2011). Link, Google ScholarN. C. Benson and V. Daggett, J. Bioinform. Comput. Biol. 10(4), 1250008 (2012). Link, Google ScholarR. Butawita and V. Palade, J. Bioinform. Comput. Biol. 10(4), 1250003 (2012). Link, Google ScholarC. Liet al., J. Bioinform. Comput. Biol. 4(5), 1119 (2006). Link, Google ScholarS. Ramseyet al., J. Bioinform. Comput. Biol. 3(2), 415 (2005). Link, Google ScholarD. Calcadaet al., J. Bioinform. Comput. Biol. 9(5), 613 (2011). Link, Google ScholarB. Liu and P. S. Thiagarajan, J. Bioinform. Comput. Biol. 10(4), 1231001 (2012). Link, Google Scholar FiguresReferencesRelatedDetailsCited By 1A study of the lipid-mediated dimerization of the RAGE TM+JM domains by molecular dynamic simulationsJialin Chen, Fude Sun, Peng Chen, Mengya Chai and Lida Xu et al.1 Jul 2018 | Chinese Chemical Letters, Vol. 29, No. 7 Recommended Vol. 10, No. 04 Metrics History PDF download

Sonorant transparency and the complexity of voicing in Polish

Final devoicing and regressive voice assimilation have been reported to apply to obstruents in word-final obstruent+sonorant clusters in Polish. This phenomenon, interpreted as a case of sonorant transparency in generative phonological analyses of Polish voicing, has sparked a number of attempts to reconcile the transparency generalisation with phonological characteristics of other laryngeal processes in Polish. This paper formulates some predictions concerning the surface realisation of underlying voicing values that follow from the sonorant transparency hypothesis, and reports on a production experiment designed to test these predictions. Results show, contrary to the descriptive and theoretical literature, that word-final sonorants typically block final devoicing and voice assimilation. The minority of cases where voicing and devoicing appear to apply as predicted by transparency are analysed using mixed-effects modelling, with a view to determining what factors influence their occurrence. Based on the results it is argued that apparent transparency cases are best explained as resulting from an interaction of phonological, phonetic and lexical factors, including manner of articulation, segmental duration, prosodic boundary, and word size, which are known to affect the probability of vocal fold vibration, and that systematic phonetic variation found in the data does not support the hypothesis that sonorants are transparent to laryngeal processes.

Lexical Evaluation of Teacher-made Coursebooks: Thai Case Studies of Foundation English Courses at Tertiary Level

Coursebooks as one of the major issues of language teaching / learning instruction can relieve the overburden as well as under-prepared teacher of a great deal of stress, time and additional work. Currently, both commercial and teacher-made English language teaching (ELT) coursebooks are available for use and seem flexible at hands. In any respect, however, usefulness of the coursebooks needs to be evaluated as claimed. To this end, the study, proposed as a new approach to lexical evaluation, examines the words occurring in three teacher-made ELT coursebooks used for compulsory foundation English courses in a Thai university as lexical syllabi are required to prepare university students for academic study at tertiary level. The RANGE program was employed to analyze the wordlists of the three teacher-made ELT coursebooks and it was found that those ELT coursebooks provided insufficient vocabulary size of general service words and academic words which were crucial to academic study regardless of syntactic structures. In addition, the three ELT coursebooks were frustrated for learners to survive unassisted reading in and outside the class. Application and suggestions are given for concerns and pedagogical practices.

Circulation: Cardiovascular Quality and Outcomes Annual Report, 2012

With this issue, we mark 4 complete years of publication of Circulation: Cardiovascular Quality and Outcomes (CQO). Thank you to our editors, readers, authors, reviewers, and supporters—and especially to Emily Picillo, Katie Sullivan, Karen Barry, and the rest of the outstanding Circulation staff—for helping CQO to mature as a publication with impact. Earlier this year, we submitted a report to the Scientific Publishing Committee of the American Heart Association. We would like to share the key aspects of the report. The mission of CQO is to improve clinical care and healthcare delivery for patients with, or at risk for, cardiovascular disease and stroke. We pursue this mission through a format that promotes scholarship, education, and constructive debate. The audience includes researchers, clinicians, policymakers, administrators, health plan executives, and government agency professionals. In addition to serving as a venue for high-quality scholarship, we seek to be a catalyst for good science, a vehicle for strengthening and expanding the community that is committed to improving clinical care and population health, and a means to inspire junior investigators to engage in scholarly activities of consequence. CQO has included original research, methods (describing studies that have been implemented) and methodological (describing specific research methods) articles, commentaries, data reports, quality improvement articles, and editorial perspectives. Our original articles span a broad set of disciplines. We consider the journal to be a home for high-quality epidemiology studies that have relevance for patient outcomes and public health. In a word cloud from the titles of 100 articles published in CQO earlier in the year (Figure 1), with word size proportionate to frequency of use, it is most heartening that the largest word is patients . Figure 1. Word cloud created from text contained in a sample of 100 articles published in CQO in 2012. Although the impact factor, defined …

A Row-Parallel 8$\,\times\,$8 2-D DCT Architecture Using Algebraic Integer-Based Exact Computation

An algebraic integer (AI) based time-multiplexed row-parallel architecture and two final-reconstruction step (FRS) algorithms are proposed for the implementation of bivariate AI-encoded 2-D discrete cosine transform (DCT). The architecture directly realizes an error-free 2-D DCT without using FRSs between row-column transforms, leading to an 8$\times$8 2-D DCT which is entirely free of quantization errors in AI basis. As a result, the user-selectable accuracy for each of the coefficients in the FRS facilitates each of the 64 coefficients to have its precision set independently of others, avoiding the leakage of quantization noise between channels as is the case for published DCT designs. The proposed FRS uses two approaches based on (i) optimized Dempster-Macleod multipliers and (ii) expansion factor scaling. This architecture enables low-noise high-dynamic range applications in digital video processing that requires full control of the finite-precision computation of the 2-D DCT. The proposed architectures and FRS techniques are experimentally verified and validated using hardware implementations that are physically realized and verified on FPGA chip. Six designs, for 4- and 8-bit input word sizes, using the two proposed FRS schemes, have been designed, simulated, physically implemented and measured. The maximum clock rate and block-rate achieved among 8-bit input designs are 307.787 MHz and 38.47 MHz, respectively, implying a pixel rate of 8$\times$307.787$\approx$2.462 GHz if eventually embedded in a real-time video-processing system. The equivalent frame rate is about 1187.35 Hz for the image size of 1920$\times$1080. All implementations are functional on a Xilinx Virtex-6 XC6VLX240T FPGA device.