Search results for: Biological sequence

Authors: Razib M. Othman, Safaai Deris, Rosli M. Illias

Abstract:

Annotation of a protein sequence is pivotal for the understanding of its function. Accuracy of manual annotation provided by curators is still questionable by having lesser evidence strength and yet a hard task and time consuming. A number of computational methods including tools have been developed to tackle this challenging task. However, they require high-cost hardware, are difficult to be setup by the bioscientists, or depend on time intensive and blind sequence similarity search like Basic Local Alignment Search Tool. This paper introduces a new method of assigning highly correlated Gene Ontology terms of annotated protein sequences to partially annotated or newly discovered protein sequences. This method is fully based on Gene Ontology data and annotations. Two problems had been identified to achieve this method. The first problem relates to splitting the single monolithic Gene Ontology RDF/XML file into a set of smaller files that can be easy to assess and process. Thus, these files can be enriched with protein sequences and Inferred from Electronic Annotation evidence associations. The second problem involves searching for a set of semantically similar Gene Ontology terms to a given query. The details of macro and micro problems involved and their solutions including objective of this study are described. This paper also describes the protein sequence annotation and the Gene Ontology. The methodology of this study and Gene Ontology based protein sequence annotation tool namely extended UTMGO is presented. Furthermore, its basic version which is a Gene Ontology browser that is based on semantic similarity search is also introduced.

Keywords: automatic clustering, bioinformatics tool, gene ontology, protein sequence annotation, semantic similarity search

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Authors: T. Holden, G. Tremberger, Jr, E. Cheung, R. Subramaniam, R. Sullivan, N. Gadura, P. Schneider, P. Marchese, A. Flamholz, T. Cheung, D. Lieberman

Abstract:

A nucleotide sequence can be expressed as a numerical sequence when each nucleotide is assigned its proton number. A resulting gene numerical sequence can be investigated for its fractal dimension in terms of evolution and chemical properties for comparative studies. We have investigated such nucleotide fluctuation in the 16S rRNA gene of archaea thermophiles. The studied archaea thermophiles were archaeoglobus fulgidus, methanothermobacter thermautotrophicus, methanocaldococcus jannaschii, pyrococcus horikoshii, and thermoplasma acidophilum. The studied five archaea-euryarchaeota thermophiles have fractal dimension values ranging from 1.93 to 1.97. Computer simulation shows that random sequences would have an average of about 2 with a standard deviation about 0.015. The fractal dimension was found to correlate (negative correlation) with the thermophile-s optimal growth temperature with R2 value of 0.90 (N =5). The inclusion of two aracheae-crenarchaeota thermophiles reduces the R2 value to 0.66 (N = 7). Further inclusion of two bacterial thermophiles reduces the R2 value to 0.50 (N =9). The fractal dimension is correlated (positive) to the sequence GC content with an R2 value of 0.89 for the five archaea-euryarchaeota thermophiles (and 0.74 for the entire set of N = 9), although computer simulation shows little correlation. The highest correlation (positive) was found to be between the fractal dimension and di-nucleotide Shannon entropy. However Shannon entropy and sequence GC content were observed to correlate with optimal growth temperature having an R2 of 0.8 (negative), and 0.88 (positive), respectively, for the entire set of 9 thermophiles; thus the correlation lacks species specificity. Together with another correlation study of bacterial radiation dosage with RecA repair gene sequence fractal dimension, it is postulated that fractal dimension analysis is a sensitive tool for studying the relationship between genotype and phenotype among closely related sequences.

Keywords: Fractal dimension, archaea thermophiles, Shannon entropy, GC content

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Authors: Jihyung Kim, Taejin Kim, Sungho Park, Jun-Dong Cho

Abstract:

In this paper, we address the problem of reducing the switching activity (SA) in on-chip buses through the use of a bus binding technique in high-level synthesis. While many binding techniques to reduce the SA exist, we present yet another technique for further reducing the switching activity. Our proposed method combines bus binding and data sequence reordering to explore a wider solution space. The problem is formulated as a multiple traveling salesman problem and solved using simulated annealing technique. The experimental results revealed that a binding solution obtained with the proposed method reduces 5.6-27.2% (18.0% on average) and 2.6-12.7% (6.8% on average) of the switching activity when compared with conventional binding-only and hybrid binding-encoding methods, respectively.

Keywords: low power, bus binding, switching activity, multiple traveling salesman problem, data sequence reordering

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Authors: Thomas Jin-Chee Liu, Jin-Wei Liang, Wei-Long Chen, Teng-Hui Chen

Abstract:

The finite element analysis is adopted in this primary study. Using the Tsai-Wu criterion and delamination criterion, the stacking sequence [45/0₄/-45₄/90₄]_s is the final optimal design for the wheelchair frame. On the contrary, the uni-directional laminates, i.e. [90₁₃]_s, [45₁₃]_s and [-45₁₃]_s, are bad designs due to the higher failure indexes.

Keywords: Wheelchair frame, stacking sequence, failure index, finite element.

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Authors: Melvin A. Ballera

Abstract:

Prior literature in the field of adaptive and personalized learning sequence in e-learning have proposed and implemented various mechanisms to improve the learning process such as individualization and personalization, but complex to implement due to expensive algorithmic programming and need of extensive and prior data. The main objective of personalizing learning sequence is to maximize learning by dynamically selecting the closest teaching operation in order to achieve the learning competency of learner. In this paper, a revolutionary technique has been proposed and tested to perform individualization and personalization using modified reversed roulette wheel selection algorithm that runs at O(n). The technique is simpler to implement and is algorithmically less expensive compared to other revolutionary algorithms since it collects the dynamic real time performance matrix such as examinations, reviews, and study to form the RWSA single numerical fitness value. Results show that the implemented system is capable of recommending new learning sequences that lessens time of study based on student's prior knowledge and real performance matrix.

Keywords: E-learning, fitness value, personalized learning sequence, reversed roulette wheel selection algorithms.

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Authors: First G.M. Karthik, Second Ramachandra.V.Pujeri, Dr.

Abstract:

Generalized Center String (GCS) problem are generalized from Common Approximate Substring problem and Common substring problems. GCS are known to be NP-hard allowing the problems lies in the explosion of potential candidates. Finding longest center string without concerning the sequence that may not contain any motifs is not known in advance in any particular biological gene process. GCS solved by frequent pattern-mining techniques and known to be fixed parameter tractable based on the fixed input sequence length and symbol set size. Efficient method known as Bpriori algorithms can solve GCS with reasonable time/space complexities. Bpriori 2 and Bpriori 3-2 algorithm are been proposed of any length and any positions of all their instances in input sequences. In this paper, we reduced the time/space complexity of Bpriori algorithm by Constrained Based Frequent Pattern mining (CBFP) technique which integrates the idea of Constraint Based Mining and FP-tree mining. CBFP mining technique solves the GCS problem works for all center string of any length, but also for the positions of all their mutated copies of input sequence. CBFP mining technique construct TRIE like with FP tree to represent the mutated copies of center string of any length, along with constraints to restraint growth of the consensus tree. The complexity analysis for Constrained Based FP mining technique and Bpriori algorithm is done based on the worst case and average case approach. Algorithm's correctness compared with the Bpriori algorithm using artificial data is shown.

Keywords: Constraint Based Mining, FP tree, Data mining, GCS problem, CBFP mining technique.

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Authors: K. Kemih, M. Benslama

Abstract:

This paper investigates the problem of spreading sequence and receiver code synchronization techniques for satellite based CDMA communications systems. The performance of CDMA system depends on the autocorrelation and cross-correlation properties of the used spreading sequences. In this paper we propose the uses of chaotic Lu system to generate binary sequences for spreading codes in a direct sequence spread CDMA system. To minimize multiple access interference (MAI) we propose the use of genetic algorithm for optimum selection of chaotic spreading sequences. To solve the problem of transmitter-receiver synchronization, we use the passivity controls. The concept of semipassivity is defined to find simple conditions which ensure boundedness of the solutions of coupled Lu systems. Numerical results are presented to show the effectiveness of the proposed approach.

Keywords: About Chaotic Lu system, synchronization, Spreading sequence, Genetic Algorithm. Passive System

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Authors: Benjamin Y. M. Kwan, Jennifer Y. Y. Kwan, Hon Keung Kwan

Abstract:

In the paper, the relative performances on spectral classification of short exon and intron sequences of the human and eleven model organisms is studied. In the simulations, all combinations of sixteen one-sequence numerical representations, four threshold values, and four window lengths are considered. Sequences of 150-base length are chosen and for each organism, a total of 16,000 sequences are used for training and testing. Results indicate that an appropriate combination of one-sequence numerical representation, threshold value, and window length is essential for arriving at top spectral classification results. For fixed-length sequences, the precisions on exon and intron classification obtained for different organisms are not the same because of their genomic differences. In general, precision increases as sequence length increases.

Keywords: Exons and introns classification, Human genome, Model organism genome, Spectral analysis

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Authors: Dalanya Asaad Mohammed, Dara Abdul Razaq

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A total of twenty tensile biopsies were collected from children undergoing tonsillectomy from teaching hospital ENT department and Kurdistan private hospital in sulaimani city. All biopsies were homogenized and cultured; the obtained bacterial isolates were purified and identified by biochemical tests and VITEK 2 compact system. Among the twenty studied samples, only one Pseudomonas putida with probability of 99% was isolated. Antimicrobial susceptibility was carried out by disk diffusion method, Pseudomonas putida showed resistance to all antibiotics used except vancomycin. The isolate further subjected to PCR and DNA sequence analysis of blaVIM gene using different set of primers for different regions of VIM gene. The results were found to be PCR positive for the blaVIM gene. To determine the sequence of blaVIM gene, DNA sequencing performed. Sequence alignment of blaVIM gene with previously recorded blaVIM gene in NCBI- database showed that P. putida isolate have different blaVIM gene.

Keywords: Clinical isolates, Putida, Sulaimani, Vim gene.

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Authors: Yi-Zhong Weng, Chien-Kang Huang, Yu-Feng Huang, Chi-Yuan Yu, Darby Tien-Hao Chang

Abstract:

Search for a tertiary substructure that geometrically matches the 3D pattern of the binding site of a well-studied protein provides a solution to predict protein functions. In our previous work, a web server has been built to predict protein-ligand binding sites based on automatically extracted templates. However, a drawback of such templates is that the web server was prone to resulting in many false positive matches. In this study, we present a sequence-order constraint to reduce the false positive matches of using automatically extracted templates to predict protein-ligand binding sites. The binding site predictor comprises i) an automatically constructed template library and ii) a local structure alignment algorithm for querying the library. The sequence-order constraint is employed to identify the inconsistency between the local regions of the query protein and the templates. Experimental results reveal that the sequence-order constraint can largely reduce the false positive matches and is effective for template-based binding site prediction.

Keywords: Protein structure, binding site, functional prediction

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Authors: Mohammad Mirabi

Abstract:

Flow-shop scheduling problem (FSP) deals with the scheduling of a set of jobs that visit a set of machines in the same order. The FSP is NP-hard, which means that an efficient algorithm for solving the problem to optimality is unavailable. To meet the requirements on time and to minimize the make-span performance of large permutation flow-shop scheduling problems in which there are sequence dependent setup times on each machine, this paper develops one hybrid genetic algorithms (HGA). Proposed HGA apply a modified approach to generate population of initial chromosomes and also use an improved heuristic called the iterated swap procedure to improve initial solutions. Also the author uses three genetic operators to make good new offspring. The results are compared to some recently developed heuristics and computational experimental results show that the proposed HGA performs very competitively with respect to accuracy and efficiency of solution.

Keywords: Hybrid genetic algorithm, Scheduling, Permutationflow-shop, Sequence dependent

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Authors: Varin Chouvatut, Suthep Madarasmi, Mihran Tuceryan

Abstract:

This paper aims to propose a novel, robust, and simple method for obtaining a human 3D face model and camera pose (position and orientation) from a video sequence. Given a video sequence of a face recorded from an off-the-shelf digital camera, feature points used to define facial parts are tracked using the Active- Appearance Model (AAM). Then, the face-s 3D structure and camera pose of each video frame can be simultaneously calculated from the obtained point correspondences. This proposed method is primarily based on the combined approaches of Gradient Descent and Powell-s Multidimensional Minimization. Using this proposed method, temporarily occluded point including the case of self-occlusion does not pose a problem. As long as the point correspondences displayed in the video sequence have enough parallax, these missing points can still be reconstructed.

Keywords: Camera Pose, Face Reconstruction, Gradient Descent, Powell's Multidimensional Minimization.

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Authors: Michele Sinico

Abstract:

In the Giovanelli illusion, some collinear dots appear misaligned, when each dot lies within a circle and the circles are not collinear. In this illusion, the role of the frame of reference, determined by the circles, is considered a crucial factor. Three experiments were carried out to study the influence of directionality of the circles on the misalignment. The adjustment method was used. Participants changed the orthogonal position of each dot, from the left to the right of the sequence, until a collinear sequence of dots was achieved. The first experiment verified the illusory effect of the misalignment. In the second experiment, the influence of two different directionalities of the circles (-0.58° and +0.58°) on the misalignment was tested. The results show an over-normalization on the sequences of the dots. The third experiment tested the misalignment of the dots without any inclination of the sequence of circles (0°). Only a local illusory effect was found. These results demonstrate that the directionality of the circles, as a global factor, can increase the misalignment. The findings also indicate that directionality and the frame of reference are independent factors in explaining the Giovanelli illusion.

Keywords: Giovanelli illusion, visual illusion, directionality, misalignment, frame of reference.

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Authors: Antonio Di Leva, Roberto Berchi, Gianpiero Pescarmona, Michele Sonnessa

Abstract:

The aim of a biological model is to understand the integrated structure and behavior of complex biological systems as a function of the underlying molecular networks to achieve simulation and forecast of their operation. Although several approaches have been introduced to take into account structural and environment related features, relatively little attention has been given to represent the behavior of biological systems. The Abstract Biological Process (ABP) model illustrated in this paper is an object-oriented model based on UML (the standard object-oriented language). Its main objective is to bring into focus the functional aspects of the biological system under analysis.

Keywords: Biological processes, system dynamics, systemmodeling, UML.

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Authors: Jinghua Zhang, Charles B. Owen, Jinsheng Xu

Abstract:

A new hybrid coding method for compressing animated polygonal meshes is presented. This paper assumes the simplistic representation of the geometric data: a temporal sequence of polygonal meshes for each discrete frame of the animated sequence. The method utilizes a delta coding and an octree-based method. In this hybrid method, both the octree approach and the delta coding approach are applied to each single frame in the animation sequence in parallel. The approach that generates the smaller encoded file size is chosen to encode the current frame. Given the same quality requirement, the hybrid coding method can achieve much higher compression ratio than the octree-only method or the delta-only method. The hybrid approach can represent 3D animated sequences with higher compression factors while maintaining reasonable quality. It is easy to implement and have a low cost encoding process and a fast decoding process, which make it a better choice for real time application.

Keywords: animated polygonal meshes, compression, deltacoding, octree.

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Authors: Javad Abdalkhani

Abstract:

Convergence of power series solutions for a class of non-linear Abel type equations, including an equation that arises in nonlinear cooling of semi-infinite rods, is very slow inside their small radius of convergence. Beyond that the corresponding power series are wildly divergent. Implementation of nonlinear sequence transformation allow effortless evaluation of these power series on very large intervals..

Keywords: Nonlinear transformation, Abel Volterra Equations, Mathematica

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Authors: JiEun Jeong, Se-Won Kang, Hee-Ju Hwang, Sung-Hwa Chae, Sang-Haeng Choi, Hong-SeogPark, YeonSoo Han, Bok-Reul Lee, Dae-Hyun Seog, Yong Seok Lee

Abstract:

Tofurther advance research on immune-related genes from T. molitor, we constructed acDNA library and analyzed expressed sequence taq (EST) sequences from 1,056 clones. After removing vector sequence and quality checkingthrough thePhred program (trim_alt 0.05 (P-score>20), 1039 sequences were generated. The average length of insert was 792 bp. In addition, we identified 162 clusters, 167 contigs and 391 contigs after clustering and assembling process using a TGICL package. EST sequences were searchedagainst NCBI nr database by local BLAST (blastx, EKeywords: EST, Innate immunity, Tenebriomolitor

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Authors: Ghada Badr, Arwa Alturki

Abstract:

The biological function of an RNA molecule depends on its structure. The objective of the alignment is finding the homology between two or more RNA secondary structures. Knowing the common functionalities between two RNA structures allows a better understanding and a discovery of other relationships between them. Besides, identifying non-coding RNAs -that is not translated into a protein- is a popular application in which RNA structural alignment is the first step A few methods for RNA structure-to-structure alignment have been developed. Most of these methods are partial structure-to-structure, sequence-to-structure, or structure-to-sequence alignment. Less attention is given in the literature to the use of efficient RNA structure representation and the structure-to-structure alignment methods are lacking. In this paper, we introduce an O(N2) Component-based Pairwise RNA Structure Alignment (CompPSA) algorithm, where structures are given as a component-based representation and where N is the maximum number of components in the two structures. The proposed algorithm compares the two RNA secondary structures based on their weighted component features rather than on their base-pair details. Extensive experiments are conducted illustrating the efficiency of the CompPSA algorithm when compared to other approaches and on different real and simulated datasets. The CompPSA algorithm shows an accurate similarity measure between components. The algorithm gives the flexibility for the user to align the two RNA structures based on their weighted features (position, full length, and/or stem length). Moreover, the algorithm proves scalability and efficiency in time and memory performance.

Keywords: Alignment, RNA secondary structure, pairwise, component-based, data mining.

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Authors: G.K.Panda, S.S.Rout

Abstract:

The balancing numbers are natural numbers n satisfying the Diophantine equation 1 + 2 + 3 + · · · + (n - 1) = (n + 1) + (n + 2) + · · · + (n + r); r is the balancer corresponding to the balancing number n.The nth balancing number is denoted by Bn and the sequence {Bn}1 n=1 satisfies the recurrence relation Bn+1 = 6Bn-Bn-1. The balancing numbers posses some curious properties, some like Fibonacci numbers and some others are more interesting. This paper is a study of recurrent sequence {xn}1 n=1 satisfying the recurrence relation xn+1 = Axn - Bxn-1 and possessing some curious properties like the balancing numbers.

Keywords: Recurrent sequences, Balancing numbers, Lucas balancing numbers, Binet form.

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Authors: M. Kusá, M. Matúšová, A. Javorová, K. Velí

Abstract:

This paper deals about four items assembly process of linear drive. This assembly will be realized in flexible assembly cell on Institute of Manufacturing Systems and Applied Mechanics. There is defined manufacturing cell, individual actuators created our flexible cell. Next chapter is about control type, detailed describe a sequence control type, which will be used in mentioned flexible assembly cell. All cell control is divided in individual steps instructions. There instructions illustrate table number III.

Keywords: assembly, flexible cell, sequence control

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Authors: R. B. Mishra

Abstract:

Hidden Markov Model (HMM) has been used in prediction and determination of states that generate different neural activations as well as mental working conditions. This paper addresses two applications of HMM; one to determine the optimal sequence of states for two neural states: Active (AC) and Inactive (IA) for the three emission (observations) which are for No Working (NW), Waiting (WT) and Working (W) conditions of human beings. Another is for the determination of optimal sequence of intentionality i.e. Believe (B), Desire (D), and Intention (I) as the states and three observational sequences: NW, WT and W. The computational results are encouraging and useful.

Keywords: BDI, HMM, neural activation, optimal states, working conditions.

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Authors: M. Sadeghi, H. Pezeshk, R. Tusserkani, A. Sharifi Zarchi, A. Malekpour, M. Foroughmand, S. Goliaei, M. Totonchi, N. Ansari–Pour

Abstract:

The role and relative importance of intrinsic and extrinsic factors in the development of complex diseases such as cancer still remains a controversial issue. Determining the amount of variation explained by these factors needs experimental data and statistical models. These models are nevertheless based on the occurrence and accumulation of random mutational events during stem cell division, thus rendering cancer development a stochastic outcome. We demonstrate that not only individual genome sequencing is uninformative in determining cancer risk, but also assigning a unique genome sequence to any given individual (healthy or affected) is not meaningful. Current whole-genome sequencing approaches are therefore unlikely to realize the promise of personalized medicine. In conclusion, since genome sequence differs from cell to cell and changes over time, it seems that determining the risk factor of complex diseases based on genome sequence is somewhat unrealistic, and therefore, the resulting data are likely to be inherently uninformative.

Keywords: Cancer risk, extrinsic factors, genome sequencing, intrinsic factors.

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Authors: S. Piramu Kailasam

Abstract:

This study is expected to compress true color image with compression algorithms in color spaces to provide high compression rates. The need of high compression ratio is to improve storage space. Alternative aim is to rank compression algorithms in a suitable color space. The dataset is sequence of true color images with size 128 x 128. HAAR Wavelet is one of the famous wavelet transforms, has great potential and maintains image quality of color images. HAAR wavelet Transform using Set Partitioning in Hierarchical Trees (SPIHT) algorithm with different color spaces framework is applied to compress sequence of images with angles. Embedded Zerotrees of Wavelet (EZW) is a powerful standard method to sequence data. Hence the proposed compression frame work of HAAR wavelet, xyz color space, morphological gradient and applied image with EZW compression, obtained improvement to other methods, in terms of Compression Ratio, Mean Square Error, Peak Signal Noise Ratio and Bits Per Pixel quality measures.

Keywords: Color Spaces, HAAR Wavelet, Morphological Gradient, Embedded Zerotrees Wavelet Compression.

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Authors: Raju Bhukya, DVLN Somayajulu

Abstract:

Pattern matching is one of the fundamental applications in molecular biology. Searching DNA related data is a common activity for molecular biologists. In this paper we explore the applicability of a new pattern matching technique called Index based Forward Backward Multiple Pattern Matching algorithm(IFBMPM), for DNA Sequences. Our approach avoids unnecessary comparisons in the DNA Sequence due to this; the number of comparisons of the proposed algorithm is very less compared to other existing popular methods. The number of comparisons rapidly decreases and execution time decreases accordingly and shows better performance.

Keywords: Comparisons, DNA Sequence, Index.

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Authors: Jafar Ahmadi, Zhohreh Asiaban, Sedigheh Fabriki Ourang

Abstract:

Brassinosteroids (BRs) regulate cell elongation, vascular differentiation, senescence, and stress responses. BRs signal through the BES1/BZR1 family of transcription factors, which regulate hundreds of target genes involved in this pathway. In this research a comprehensive genome-wide analysis was carried out in BES1/BZR1 gene family in Arabidopsis thaliana, Cucumis sativus, Vitis vinifera, Glycin max and Brachypodium distachyon. Specifications of the desired sequences, dot plot and hydropathy plot were analyzed in the protein and genome sequences of five plant species. The maximum amino acid length was attributed to protein sequence Brdic3g with 374aa and the minimum amino acid length was attributed to protein sequence Gm7g with 163aa. The maximum Instability index was attributed to protein sequence AT1G19350 equal with 79.99 and the minimum Instability index was attributed to protein sequence Gm5g equal with 33.22. Aliphatic index of these protein sequences ranged from 47.82 to 78.79 in Arabidopsis thaliana, 49.91 to 57.50 in Vitis vinifera, 55.09 to 82.43 in Glycin max, 54.09 to 54.28 in Brachypodium distachyon 55.36 to 56.83 in Cucumis sativus. Overall, data obtained from our investigation contributes a better understanding of the complexity of the BES1/BZR1 gene family and provides the first step towards directing future experimental designs to perform systematic analysis of the functions of the BES1/BZR1 gene family.

Keywords: BES1/BZR1, Brassinosteroids, Phylogenetic analysis, Transcription factor.

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Authors: L. Parisi, D. Hamili, N. Azlan

Abstract:

The aim of this study was to design and simulate a particular type of Asynchronous State Machine (ASM), namely a ‘traffic light controller’ (TLC), operated at a frequency of 0.5 Hz. The design task involved two main stages: firstly, designing a 4-bit binary counter using J-K flip flops as the timing signal and, subsequently, attaining the digital logic by deploying ASM design process. The TLC was designed such that it showed a sequence of three different colours, i.e. red, yellow and green, corresponding to set thresholds by deploying the least number of AND, OR and NOT gates possible. The software Multisim was deployed to design such circuit and simulate it for circuit troubleshooting in order for it to display the output sequence of the three different colours on the traffic light in the correct order. A clock signal, an asynchronous 4- bit binary counter that was designed through the use of J-K flip flops along with an ASM were used to complete this sequence, which was programmed to be repeated indefinitely. Eventually, the circuit was debugged and optimized, thus displaying the correct waveforms of the three outputs through the logic analyser. However, hazards occurred when the frequency was increased to 10 MHz. This was attributed to delays in the feedback being too high.

Keywords: Asynchronous State Machine, Traffic Light Controller, Circuit Design, Digital Electronics.

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Authors: S. Sowmyayani, P. Arockia Jansi Rani

Abstract:

This paper integrates Octagon and Square Search pattern (OCTSS) motion estimation algorithm into H.264/AVC (Advanced Video Coding) video codec in Adaptive Group of Pictures (AGOP) mode. AGOP structure is computed based on scene change in the video sequence. Octagon and square search pattern block-based motion estimation method is implemented in inter-prediction process of H.264/AVC. Both these methods reduce bit rate and computational complexity while maintaining the quality of the video sequence respectively. Experiments are conducted for different types of video sequence. The results substantially proved that the bit rate, computation time and PSNR gain achieved by the proposed method is better than the existing H.264/AVC with fixed GOP and AGOP. With a marginal gain in quality of 0.28dB and average gain in bitrate of 132.87kbps, the proposed method reduces the average computation time by 27.31 minutes when compared to the existing state-of-art H.264/AVC video codec.

Keywords: Block Distortion Measure, Block Matching Algorithms, H.264/AVC, Motion estimation, Search patterns, Shot cut detection.

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Authors: Hsing-Kuo Pao, John Case

Abstract:

Biological sequences from different species are called or-thologs if they evolved from a sequence of a common ancestor species and they have the same biological function. Approximations of Kolmogorov complexity or entropy of biological sequences are already well known to be useful in extracting similarity information between such sequences -in the interest, for example, of ortholog detection. As is well known, the exact Kolmogorov complexity is not algorithmically computable. In prac-tice one can approximate it by computable compression methods. How-ever, such compression methods do not provide a good approximation to Kolmogorov complexity for short sequences. Herein is suggested a new ap-proach to overcome the problem that compression approximations may notwork well on short sequences. This approach is inspired by new, conditional computations of Kolmogorov entropy. A main contribution of the empir-ical work described shows the new set of entropy-based machine learning attributes provides good separation between positive (ortholog) and nega-tive (non-ortholog) data - better than with good, previously known alter-natives (which do not employ some means to handle short sequences well).Also empirically compared are the new entropy based attribute set and a number of other, more standard similarity attributes sets commonly used in genomic analysis. The various similarity attributes are evaluated by cross validation, through boosted decision tree induction C5.0, and by Receiver Operating Characteristic (ROC) analysis. The results point to the conclu-sion: the new, entropy based attribute set by itself is not the one giving the best prediction; however, it is the best attribute set for use in improving the other, standard attribute sets when conjoined with them.

Keywords: compression, decision tree, entropy, ortholog, ROC.

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Authors: M. T. Yazdani Sabouni, Rasaratnam Logendran

Abstract:

We consider a typical problem in the assembly of printed circuit boards (PCBs) in a two-machine flow shop system to simultaneously minimize the weighted sum of weighted tardiness and weighted flow time. The investigated problem is a group scheduling problem in which PCBs are assembled in groups and the interest is to find the best sequence of groups as well as the boards within each group to minimize the objective function value. The type of setup operation between any two board groups is characterized as carryover sequence-dependent setup time, which exactly matches with the real application of this problem. As a technical constraint, all of the boards must be kitted before the assembly operation starts (kitting operation) and by kitting staff. The main idea developed in this paper is to completely eliminate the role of kitting staff by assigning the task of kitting to the machine operator during the time he is idle which is referred to as integration of internal (machine) and external (kitting) setup times. Performing the kitting operation, which is a preparation process of the next set of boards while the other boards are currently being assembled, results in the boards to continuously enter the system or have dynamic arrival times. Consequently, a dynamic PCB assembly system is introduced for the first time in the assembly of PCBs, which also has characteristics similar to that of just-in-time manufacturing. The problem investigated is computationally very complex, meaning that finding the optimal solutions especially when the problem size gets larger is impossible. Thus, a heuristic based on Genetic Algorithm (GA) is employed. An example problem on the application of the GA developed is demonstrated and also numerical results of applying the GA on solving several instances are provided.

Keywords: Genetic algorithm, Dynamic PCB assembly, Carryover sequence-dependent setup times, Multi-objective.

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Authors: Shin-Shin Kao, Hsiu-Chunj Pan

Abstract:

Given a graph G. A cycle of G is a sequence of vertices of G such that the first and the last vertices are the same. A hamiltonian cycle of G is a cycle containing all vertices of G. The graph G is k-ordered (resp. k-ordered hamiltonian) if for any sequence of k distinct vertices of G, there exists a cycle (resp. hamiltonian cycle) in G containing these k vertices in the specified order. Obviously, any cycle in a graph is 1-ordered, 2-ordered and 3- ordered. Thus the study of any graph being k-ordered (resp. k-ordered hamiltonian) always starts with k = 4. Most studies about this topic work on graphs with no real applications. To our knowledge, the chordal ring families were the first one utilized as the underlying topology in interconnection networks and shown to be 4-ordered. Furthermore, based on our computer experimental results, it was conjectured that some of them are 4-ordered hamiltonian. In this paper, we intend to give some possible directions in proving the conjecture.

Keywords: Hamiltonian cycle, 4-ordered, Chordal rings, 3-regular.

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