Search results for: sequence evolution

Authors: Dong Tran, Thanh Dac Van, Ly Le

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Hemagglutinin (HA) and Neuraminidase (NA) play an important role in host immune evasion across influenza virus evolution process. The correlation between HA and NA evolution in respect to epitopic evolution and drug interaction has yet to be investigated. In this study, combining of sequence to structure evolution and statistical analysis on epitopic/binding site specificity, we identified potential therapeutic features of HA and NA that show specific antibody binding site of HA and specific binding distribution within NA active site of current inhibitors. Our approach introduces the use of sequence variation and molecular interaction to provide an effective strategy in establishing experimental based distributed representations of protein-protein/ligand complexes. The most important advantage of our method is that it does not require complete dataset of complexes but rather directly inferring feature interaction from sequence variation and molecular interaction. Using correlated sequence analysis, we additionally identified co-evolved mutations associated with maintaining HA/NA structural and functional variability toward immunity and therapeutic treatment. Our investigation on the HA binding specificity revealed unique conserved stalk domain interacts with unique loop domain of universal antibodies (CR9114, CT149, CR8043, CR8020, F16v3, CR6261, F10). On the other hand, NA inhibitors (Oseltamivir, Zaninamivir, Laninamivir) showed specific conserved residue contribution and similar to that of NA substrate (sialic acid) which can be exploited for drug design. Our study provides an important insight into rational design and identification of novel therapeutics targeting universally recognized feature of influenza HA/NA.

Keywords: influenza virus, hemagglutinin (HA), neuraminidase (NA), sequence evolution

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Authors: Seyyd Hossein Jafari-Petroudi, Maryam Pirouz

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This note is devoted to (k; h)-Jacobsthal sequence as a general term of particular series. More formulas for nth term and sum of the first n terms of series that their general terms are (k; h)-Jacobsthal sequence and (k; h)-Jacobsthal-Petroudi sequence are derived. Finally other properties of these sequences are represented.

Keywords: (k, h)-Jacobsthal sequence, (k, h)-Jacobsthal Petroudisequence, recursive relation, sum

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Authors: Viriyavudh Sim, SeungHyun Kim, JungKyu Choi, WooYoung Jung

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Glass Fiber Reinforced Polymer (GFRP) is a major evolution for energy dissipation when used as infill material for seismic retrofitting of steel frame, a basic PMC infill wall system consists of two GFRP laminates surrounding an infill of foam core. This paper presents numerical analysis in terms of buckling resistance of GFRP sandwich infill panels system under the influence of environment temperature and stacking sequence of laminate skin. Mode of failure under in-plane compression is studied by means of numerical analysis with ABAQUS platform. Parameters considered in this study are contact length between infill and frame, laminate stacking sequence of GFRP skin and variation of mechanical properties due to increment of temperature. The analysis is done with four cases of simple stacking sequence over a range of temperature. The result showed that both the effect of temperature and stacking sequence alter the performance of entire panel system. The rises of temperature resulted in the decrements of the panel’s strength. This is due to the polymeric nature of this material. Additionally, the contact length also displays the effect on the performance of infill panel. Furthermore, the laminate stiffness can be modified by orientation of laminate, which can increase the infill panel strength. Hence, optimal performance of the entire panel system can be obtained by comparing different cases of stacking sequence.

Keywords: buckling resistance, GFRP infill panel, stacking sequence, temperature dependent

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Authors: Khaled Jaber

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The estimation of effort in software development is a complex task. The traditional Waterfall approach used to develop software systems requires a lot of time to estimate the effort needed to implement user requirements. Agile manifesto, however, is currently more used in the industry than the Waterfall to develop software systems. In Agile, the user requirement is referred to as a user story. Agile teams mostly use the Fibonacci sequence 1, 2, 3, 5, 8, 11, etc. in estimating the effort needed to implement the user story. This work shows through analysis that the Arithmetic sequence, e.g., 3, 6, 9, 12, etc., is more effective than the Fibonacci sequence in estimating the user stories. This paper mathematically and visually proves the effectiveness of the Arithmetic sequence over the FB sequence.

Keywords: agie, scrum, estimation, fibonacci sequence

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Authors: Rajkumar Ghosh

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The Chaura Thrust, located in Himachal Pradesh, India, is a prominent geological feature that exhibits characteristics of an out-of-sequence thrust fault. This paper explores the geological setting of Himachal Pradesh, focusing on the Chaura Thrust's unique characteristics, its classification as an out-of-sequence thrust, and the implications of its presence in the region. The introduction provides background information on thrust faults and out-of-sequence thrusts, emphasizing their significance in understanding the tectonic history and deformation patterns of an area. It also outlines the objectives of the paper, which include examining the Chaura Thrust's geological features, discussing its classification as an out-of-sequence thrust, and assessing its implications for the region. The paper delves into the geological setting of Himachal Pradesh, describing the tectonic framework and providing insights into the formation of thrust faults in the region. Special attention is given to the Chaura Thrust, including its location, extent, and geometry, along with an overview of the associated rock formations and structural characteristics. The concept of out-of-sequence thrusts is introduced, defining their distinctive behavior and highlighting their importance in the understanding of geological processes. The Chaura Thrust is then analyzed in the context of an out-of-sequence thrust, examining the evidence and characteristics that support this classification. Factors contributing to the out-of-sequence behavior of the Chaura Thrust, such as stress interactions and fault interactions, are discussed. The geological implications and significance of the Chaura Thrust are explored, addressing its impact on the regional geology, tectonic evolution, and seismic hazard assessment. The paper also discusses the potential geological hazards associated with the Chaura Thrust and the need for effective mitigation strategies in the region. Future research directions and recommendations are provided, highlighting areas that warrant further investigation, such as detailed structural analyses, geodetic measurements, and geophysical surveys. The importance of continued research in understanding and managing geological hazards related to the Chaura Thrust is emphasized. In conclusion, the Chaura Thrust in Himachal Pradesh represents an out-of-sequence thrust fault that has significant implications for the region's geology and tectonic evolution. By studying the unique characteristics and behavior of the Chaura Thrust, researchers can gain valuable insights into the geological processes occurring in Himachal Pradesh and contribute to a better understanding and mitigation of seismic hazards in the area.

Keywords: chaura thrust, out-of-sequence thrust, himachal pradesh, geological setting, tectonic framework, rock formations, structural characteristics, stress interactions, fault interactions, geological implications, seismic hazard assessment, geological hazards, future research, mitigation strategies.

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Authors: Bouras Zine Eddine, Talai Abdelouaheb

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The need to merge software artifacts seems inherent to modern software development. Distribution of development over several teams and breaking tasks into smaller, more manageable pieces are an effective means to deal with the kind of complexity. In each case, the separately developed artifacts need to be assembled as efficiently as possible into a consistent whole in which the parts still function as described. Also, earlier changes are introduced into the life cycle and easier is their management by designers. Interaction-based specifications such as UML sequence diagrams have been found effective in this regard. As a result, sequence diagrams can be used not only for capturing system behaviors but also for merging changes in order to create a new version. The objective of this paper is to suggest a new approach to deal with the problem of software merging at the level of sequence diagrams by using the concept of dependence analysis that captures, formally, all mapping and differences between elements of sequence diagrams and serves as a key concept to create a new version of sequence diagram.

Keywords: system behaviors, sequence diagram merging, dependence analysis, sequence diagram slicing

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Authors: Subhayan Maity

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Complete scenario of cosmic evolution from emergent phase to late time acceleration (i.e. non-singular ever expanding Universe) is a popular preference in the recent cosmology. Yet one can’t exclude the idea that other type of evolution pattern of the Universe may also be possible. Especially, the bouncing scenario is becoming a matter of interest now a days. The present work is an exhibition of such a different pattern of cosmic evolution where the evolution of Universe has been shown as a cyclic thermodynamic process. Under diffusion mechanism (non-equilibrium thermodynamic process), the cosmic evolution has been modelled as [ emergent - accelerated expansion - decelerated expansion - decelerated contraction - accelerated contraction - emergent] .

Keywords: non-equilibrium thermodynamics, non singular evolution of universe, cyclic evolution, diffusive fluid

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Authors: Iftikhar A. Tayubi, Aabdulrahman Alsubhi, Abdullah Althrwi

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The deoxyribonucleic acid text provides a single source of high-quality Cryptography about Deoxyribonucleic acid sequence for structural biologists. We will provide an intuitive, well-organized and user-friendly web interface that allows users to encrypt and decrypt Deoxy Ribonucleic Acid sequence text. It includes complex, securing by using Algorithm to encrypt and decrypt Deoxy Ribonucleic Acid sequence. The utility of this Deoxy Ribonucleic Acid Sequence Text is that, it can provide a user-friendly interface for users to Encrypt and Decrypt store the information about Deoxy Ribonucleic Acid sequence. These interfaces created in this project will satisfy the demands of the scientific community by providing fully encrypt of Deoxy Ribonucleic Acid sequence during this website. We have adopted a methodology by using C# and Active Server Page.NET for programming which is smart and secure. Deoxy Ribonucleic Acid sequence text is a wonderful piece of equipment for encrypting large quantities of data, efficiently. The users can thus navigate from one encoding and store orange text, depending on the field for user’s interest. Algorithm classification allows a user to Protect the deoxy ribonucleic acid sequence from change, whether an alteration or error occurred during the Deoxy Ribonucleic Acid sequence data transfer. It will check the integrity of the Deoxy Ribonucleic Acid sequence data during the access.

Keywords: algorithm, ASP.NET, DNA, encrypt, decrypt

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Authors: Yaw-Ling Lin

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A de Bruijn graph of order k is a graph whose vertices representing all length-k sequences with edges joining pairs of vertices whose sequences have maximum possible overlap (length k−1). Every Hamiltonian cycle of this graph defines a distinct, minimum length de Bruijn sequence containing all k-mers exactly once. A Kautz sequence is the minimal generating sequence so as the sequence of minimal length that produces all possible length-k sequences with the restriction that every two consecutive alphabets in the sequences must be different. A collection of de Bruijn/Kautz sequences are orthogonal if any two sequences are of maximally differ in sequence composition; that is, the maximum length of their common substring is k. In this paper, we discuss how such a collection of (maximal) orthogonal de Bruijn/Kautz sequences can be made and use the algorithm to build up a web application service for the synthesized DNA and other related biomolecular sequences.

Keywords: biomolecular sequence synthesis, de Bruijn sequences, Eulerian cycle, Hamiltonian cycle, Kautz sequences, orthogonal sequences

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Authors: Abubakar Sadiq Mensah, Hassan Usman

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The study compared the effectiveness of Audition, Multiplication, subtraction and Division (AMSD) and Addition, subtraction, Multiplication and Division (ASMD), sequence of teaching these four basic operations in mathematics to primary one pupil’s in Katsina Local Government, Katsina State. The study determined the sequence that was more effective and mostly adopted by teachers of the operations. One hundred (100) teachers and sixty pupils (60) from primary one were used for the study. The pupils were divided into two equal groups. The researcher taught these operations to each group separately for four weeks (4 weeks). Group one was taught using the ASMD sequence, while group two was taught using ASMD sequence. In order to generate the needed data for the study, questionnaires and tests were administered on the samples. Data collected were analyzed and major findings were arrived at: (i) Two primary mathematics text books were used in all the primary schools in the area; (ii) Each of the textbooks contained the ASMD sequence; (iii) 73% of the teachers sampled adopted the ASMD sequence of teaching these operations; and (iv) Group one of the pupils (taught using AMSD sequence) performed significantly better than their counter parts in group two (taught using AMSD sequence). On the basis of this, the researcher concluded that the AMSD sequence was more effective in teaching the operations than the ASMD sequence. Consequently, the researcher concluded that primary schools teachers, authors of primary mathematics textbooks, and curriculum planner should adopt the AMSD sequence of teaching these operations.

Keywords: matematic, high school, four basic operations, effectiveness of teaching

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Authors: Nazneen Khan, Vakeel A. Khan

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In this article we introduce the Paranorm Zweier I-convergent sequence spaces, for a sequence of positive real numbers. We study some topological properties, prove the decomposition theorem and study some inclusion relations on these spaces.

Keywords: ideal, filter, I-convergence, I-nullity, paranorm

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Authors: Mostefa Bendouba, Djebli Abdelkader, Abdelkrim Aid, Mohamed Benguediab

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The damage evolution mechanism is one of the important focuses of fatigue behaviour investigation of composite materials and also is the foundation to predict fatigue life of composite structures for engineering application. This paper is dedicated to a damage investigation under two block loading cycle fatigue conditions submitted to composite material. The loading sequence effect and the influence of the cycle ratio of the first stage on the cumulative fatigue life were studied herein. Two loading sequences, i.e., high-to-low and low-to-high cases are considered in this paper. The proposed damage indicator is connected cycle by cycle to the S-N curve and the experimental results are in agreement with model expectations. Some experimental researches are used to validate this proposition.

Keywords: fatigue, damage acumulation, composite, evolution

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Authors: Rajkumar Ghosh

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The study presents an overview of the many uses and approaches for estimating out-of-sequence thrust movement in earthquake mitigation. The study investigates how knowing and forecasting thrust movement during seismic occurrences might assist to effective earthquake mitigation measures. The review begins by discussing out-of-sequence thrust movement and its importance in earthquake mitigation strategies. It explores how typical techniques of estimating thrust movement may not capture the full complexity of seismic occurrences and emphasizes the benefits of include out-of-sequence data in the analysis. A thorough review of existing research and studies on out-of-sequence thrust movement estimates for earthquake mitigation. The study demonstrates how to estimate out-of-sequence thrust movement using multiple data sources such as GPS measurements, satellite imagery, and seismic recordings. The study also examines the use of out-of-sequence thrust movement estimates in earthquake mitigation measures. It investigates how precise calculation of thrust movement may help improve structural design, analyse infrastructure risk, and develop early warning systems. The potential advantages of using out-of-sequence data in these applications to improve the efficiency of earthquake mitigation techniques. The difficulties and limits of estimating out-of-sequence thrust movement for earthquake mitigation. It addresses data quality difficulties, modelling uncertainties, and computational complications. To address these obstacles and increase the accuracy and reliability of out-of-sequence thrust movement estimates, the authors recommend topics for additional study and improvement. The study is a helpful resource for seismic monitoring and earthquake risk assessment researchers, engineers, and policymakers, supporting innovations in earthquake mitigation measures based on a better knowledge of thrust movement dynamics.

Keywords: earthquake mitigation, out-of-sequence thrust, satellite imagery, seismic recordings, GPS measurements

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Authors: Muhammad A. Khan, Waseem Shahzad

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Analysis of protein sequences is carried out for the purpose to discover their structural and ancestry relationship. Sequence similarity determines similar protein structures, similar function, and homology detection. Biological sequences composed of amino acid residues or nucleotides provide significant information through sequence alignment. In this paper, we present a new similarity/dissimilarity measure to sequence alignment based on the primary structure of a protein. The approach finds the distance between the two given sequences using the novel sequence alignment algorithm and a mathematical model. The algorithm runs at a time complexity of O(n²). A distance matrix is generated to construct a phylogenetic tree of different species. The new similarity/dissimilarity measure outperforms other existing methods.

Keywords: alignment, distance, homology, mathematical model, phylogenetic tree

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Authors: András Farkas, István Molnár, Jan Vrána, Veronika Burešová, Petr Cápal, András Cseh, Márta Molnár-Láng, Jaroslav Doležel

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Species of Aegilops played a central role in the evolution of wheat and are sources of traits related to yield quality and tolerance against biotic and abiotic stresses. These wild genes and alleles are desirable to use in crop improvement programs via introgressive hybridization. However, the success of chromosome mediated gene transfer to wheat are hampered by the pour knowledge on the genome structure of Aegilops relative to wheat and by the low number of cost-effective molecular markers specific for Aegilops chromosomes. The COS markers specific for genes conserved throughout evolution in both sequence and copy number between Triticeae/Aegilops taxa and define orthologous regions, thus enabling the comparison of regions on the chromosomes of related species. The present study compared individual chromosomes of Aegilops umbellulata (UU), Ae. comosa (MM), Ae. speltoides (SS) and Ae. caudata (CC) purified by flourescent labelling with oligonucleotid SSR repeats and biparametric flow cytometry with wheat by identifying orthologous chromosomal regions by COS markers. The linear order of bin-mapped COS markers along the wheat D chromosomes was identified by the use of chromosome-specific sequence data and virtual gene order. Syntenic regions of wheat identifying genome rearrangements differentiating the U, M, S or C genomes from the D genome of wheat were detected. The conserved orthologous set markers assigned to Aegilops chromosomes promise to accelerate gene introgression by facilitating the identification of alien chromatin. The syntenic relationships between the Aegilops species and wheat will facilitate the targeted development of new markers specific for U, M, S and C genomic regions and will contribute to the understanding of molecular processes related to the evolution of Aegilops.

Keywords: Aegilops, cos-markers, flow-sorting, wheat

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Authors: Wan-Hsin Hsieh, Chieh-Fu Chang, Ming-Seng Kao

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In this paper, a novel method termed the Phase Coherence Acquisition (PCA) is proposed for pseudo-random (PN) sequence acquisition. By employing complex phasors, the PCA requires only complex additions in the order of N, the length of the sequence, whereas the conventional method utilizing fast Fourier transform (FFT) requires complex multiplications and additions both in the order of Nlog2N . In order to combat noise, the input and local sequences are partitioned and mapped into complex phasors in PCA. The phase differences between pairs of input and local phasors are utilized for acquisition, and thus complex multiplications are avoided. For more noise-robustness capability, the multi-layer PCA is developed to extract the code phase step by step. The significant reduction of computational loads makes the PCA an attractive method, especially when the sequence length of is extremely large which becomes intractable for the FFT-based acquisition.

Keywords: FFT, PCA, PN sequence, convolution theory

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Authors: Catherine K. Derow

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Possibly a slime mold somehow mutated or already was mutated at progeniture and so stayed as a metazoan when it developed into the fruiting stage and so the slime mold(s) we are evolved and similar to are genetically differ from the slime molds in existence now. This may be why there are genetic links between humans and other metazoa now alive and slime molds now alive but we are now divergent branches of the evolutionary tree compared to the original slime mold, or perhaps slime mold-like organisms, that gave rise to metazoan animalia and perhaps algae and plantae as slime molds were undifferentiated enough in many ways that could allow their descendants to evolve into these three separate phylogenetic categories. Or it may be a slime mold was born or somehow progenated as multicellular, as the particular organism was mutated enough to have say divided in a a 'pseudo-embryonic' stage, and this could have happened for algae, plantae as well as animalia or all the branches may be from the same line but the missing link might be covered in 'phylogenetic sequence comparison noise'.

Keywords: metazoan evolution, unicellular bridge to metazoans, evolution, slime mold

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Authors: Abdelati El Allaoui, Said Melliani, Lalla Saadia Chadli

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The objective of this paper is to study the existence and uniqueness of Mild solutions for a complex fuzzy evolution equation with nonlocal conditions that accommodates the notion of fuzzy sets defined by complex-valued membership functions. We first propose definition of complex fuzzy strongly continuous semigroups. We then give existence and uniqueness result relevant to the complex fuzzy evolution equation.

Keywords: Complex fuzzy evolution equations, nonlocal conditions, mild solution, complex fuzzy semigroups

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Authors: M. V. A. Raju Bahubalendruni, Bibhuti Bhusan Biswal, B. B. V. L. Deepak

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Achieving an appropriate assembly sequence needs deep verification for its physical feasibility. For this purpose, industrial engineers use several assembly predicates; namely, liaison, geometric feasibility, stability and mechanical feasibility. However, testing an assembly sequence for these predicates requires huge assembly information. Extracting such assembly information from an assembled product is a time consuming and highly skillful task with complex reasoning methods. In this paper, computer aided methods are proposed to extract all the necessary assembly information from computer aided design (CAD) environment in order to perform the assembly sequence planning efficiently. These methods use preliminary capabilities of three-dimensional solid modelling and assembly modelling methods used in CAD software considering equilibrium laws of physical bodies.

Keywords: assembly automation, assembly attributes, assembly, CAD

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Authors: Alireza Dantism

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Presently, describing the function of a protein sequence is one of the most common problems in biology. Usually, this problem can be facilitated by studying the three-dimensional structure of proteins. In the absence of a protein structure, comparative modeling often provides a useful three-dimensional model of the protein that is dependent on at least one known protein structure. Comparative modeling predicts the three-dimensional structure of a given protein sequence (target) mainly based on its alignment with one or more proteins of known structure (templates). Comparative modeling consists of four main steps 1. Similarity between the target sequence and at least one known template structure 2. Alignment of target sequence and template(s) 3. Build a model based on alignment with the selected template(s). 4. Prediction of model errors 5. Optimization of the built model There are many computer programs and web servers that automate the comparative modeling process. One of the most important advantages of these servers is that it makes comparative modeling available to both experts and non-experts, and they can easily do their own modeling without the need for programming knowledge, but some other experts prefer using programming knowledge and do their modeling manually because by doing this they can maximize the accuracy of their modeling. In this study, a web-based tool has been designed to predict the tertiary structure of proteins using PHP and Python programming languages. This tool is called EasyModel. EasyModel can receive, according to the user's inputs, the desired unknown sequence (which we know as the target) in this study, the protein sequence file (template), etc., which also has a percentage of similarity with the primary sequence, and its third structure Predict the unknown sequence and present the results in the form of graphs and constructed protein files.

Keywords: structural bioinformatics, protein tertiary structure prediction, modeling, comparative modeling, modeller

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Authors: Balamurali Gunji, B. B. V. L. Deepak, B. B. Biswal, Amrutha Rout, Golak Bihari Mohanta

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Robots play an important role in the operations like pick and place, assembly, spot welding and much more in manufacturing industries. Out of those, assembly is a very important process in manufacturing, where 20% of manufacturing cost is wholly occupied by the assembly process. To do the assembly task effectively, Assembly Sequences Planning (ASP) is required. ASP is one of the multi-objective non-deterministic optimization problems, achieving the optimal assembly sequence involves huge search space and highly complex in nature. Many researchers have followed different algorithms to solve ASP problem, which they have several limitations like the local optimal solution, huge search space, and execution time is more, complexity in applying the algorithm, etc. By keeping the above limitations in mind, in this paper, a new automated optimal robotic assembly sequence planning using Artificial Bee Colony (ABC) Algorithm is proposed. In this algorithm, automatic extraction of assembly predicates is done using Computer Aided Design (CAD) interface instead of extracting the assembly predicates manually. Due to this, the time of extraction of assembly predicates to obtain the feasible assembly sequence is reduced. The fitness evaluation of the obtained feasible sequence is carried out using ABC algorithm to generate the optimal assembly sequence. The proposed methodology is applied to different industrial products and compared the results with past literature.

Keywords: assembly sequence planning, CAD, artificial Bee colony algorithm, assembly predicates

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Authors: Sanjay Kumar Parjapati, Ajai Jain

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This paper presents optimization of makespan for ‘n’ jobs and ‘m’ machines flexible job shop scheduling problem with sequence dependent setup time using genetic algorithm (GA) approach. A restart scheme has also been applied to prevent the premature convergence. Two case studies are taken into consideration. Results are obtained by considering crossover probability (pc = 0.85) and mutation probability (pm = 0.15). Five simulation runs for each case study are taken and minimum value among them is taken as optimal makespan. Results indicate that optimal makespan can be achieved with more than one sequence of jobs in a production order.

Keywords: flexible job shop, genetic algorithm, makespan, sequence dependent setup times

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Authors: Dai Zhimei, Hua Chen

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The exploration of urban spatial evolution is an important part of urban development research. Therefore, the evolutionary modern Yangzhou urban spatial texture was taken as the research object, and Spatial Syntax was used as the main research tool, this paper explored Yangzhou spatial evolution law and its driving factors from the urban street network scale, district scale and street scale. The study has concluded that at the urban scale, Yangzhou urban spatial evolution is the result of a variety of causes, including physical and geographical condition, policy and planning factors, and traffic conditions, and the evolution of space also has an impact on social, economic, environmental and cultural factors. At the district and street scales, changes in space will have a profound influence on the history of the city and the activities of people. At the end of the article, the matters needing attention during the evolution of urban space were summarized.

Keywords: block, space syntax and methodology, street, urban space, Yangzhou

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Authors: S. H. Borghei, E. Teymourian, M. Mobin, G. M. Komaki, S. Sheikh

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Imperialist competitive algorithm (ICA) is a recent meta-heuristic method that is inspired by the social evolutions for solving NP-Hard problems. The ICA is a population based algorithm which has achieved a great performance in comparison to other meta-heuristics. This study is about developing enhanced ICA approach to solve the cell formation problem (CFP) using sequence data. In addition to the conventional ICA, an enhanced version of ICA, namely EICA, applies local search techniques to add more intensification aptitude and embed the features of exploration and intensification more successfully. Suitable performance measures are used to compare the proposed algorithms with some other powerful solution approaches in the literature. In the same way, for checking the proficiency of algorithms, forty test problems are presented. Five benchmark problems have sequence data, and other ones are based on 0-1 matrices modified to sequence based problems. Computational results elucidate the efficiency of the EICA in solving CFP problems.

Keywords: cell formation problem, group technology, imperialist competitive algorithm, sequence data

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Authors: G. Tamilpavai, C. Vishnuppriya

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Studying DNA (deoxyribonucleic acid) sequence is useful in biological processes and it is applied in the fields such as diagnostic and forensic research. DNA is the hereditary information in human and almost all other organisms. It is passed to their generations. Earlier stage detection of defective DNA sequence may lead to many developments in the field of Bioinformatics. Nowadays various tedious techniques are used to identify defective DNA. The proposed work is to analyze and identify the cancer-causing DNA motif in a given sequence. Initially the human DNA sequence is separated as k-mers using k-mer separation rule. The separated k-mers are clustered using Self Organizing Map (SOM). Using Levenshtein distance measure, cancer associated DNA motif is identified from the k-mer clusters. Experimental results of this work indicate the presence or absence of cancer causing DNA motif. If the cancer associated DNA motif is found in DNA, it is declared as the cancer disease causing DNA sequence. Otherwise the input human DNA is declared as normal sequence. Finally, elapsed time is calculated for finding the presence of cancer causing DNA motif using clustering formation. It is compared with normal process of finding cancer causing DNA motif. Locating cancer associated motif is easier in cluster formation process than the other one. The proposed work will be an initiative aid for finding genetic disease related research.

Keywords: bioinformatics, cancer motif, DNA, k-mers, Levenshtein distance, SOM

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Authors: Vyacheslav Furtak, Merja Roivainen, Olga Mirochnichenko, Majid Laassri, Bella Bidzhieva, Tatiana Zagorodnyaya, Vladimir Chizhikov, Konstantin Chumakov

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Molecular epidemiology and environmental surveillance are parts of a rational strategy to control infectious diseases. They have been widely used in the worldwide campaign to eradicate poliomyelitis, which otherwise would be complicated by the inability to rapidly respond to outbreaks and determine sources of the infection. The conventional scheme involves isolation of viruses from patients and the environment, followed by their identification by nucleotide sequences analysis to determine phylogenetic relationships. This is a tedious and time-consuming process that yields definitive results when it may be too late to implement countermeasures. Because of the difficulty of high-throughput full-genome sequencing, most such studies are conducted by sequencing only capsid genes or their parts. Therefore the important information about the contribution of other parts of the genome and inter- and intra-species recombination to viral evolution is not captured. Here we propose a new approach based on the rapid concentration of sewage samples with tangential flow filtration followed by deep sequencing and reconstruction of nucleotide sequences of viruses present in the samples. The entire nucleic acids content of each sample is sequenced, thus preserving in digital format the complete spectrum of viruses. A set of rapid algorithms was developed to separate deep sequence reads into discrete populations corresponding to each virus and assemble them into full-length consensus contigs, as well as to generate a complete profile of sequence heterogeneities in each of them. This provides an effective approach to study molecular epidemiology and evolution of natural viral populations.

Keywords: poliovirus, eradication, environmental surveillance, laboratory diagnosis

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Authors: K. Y. Tseng, C. Y. Wu

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This paper employs a heuristic algorithm to solve engineering problems including truss structure optimization and optimal chiller loading (OCL) problems. Two different type algorithms, real-valued differential evolution (DE) and modified binary differential evolution (MBDE), are successfully integrated and then can obtain better performance in solving engineering problems. In order to demonstrate the performance of the proposed algorithm, this study adopts each one testing case of truss structure optimization and OCL problems to compare the results of other heuristic optimization methods. The result indicates that the proposed algorithm can obtain similar or better solution in comparing with previous studies.

Keywords: differential evolution, Truss structure optimization, optimal chiller loading, modified binary differential evolution

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Authors: Yuhei Kunihiro, Sorin V. Sabau, Kazuhiro Shibuya

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We study the molecular evolution of insulin from the metric geometry point of view. In mathematics, and particularly in geometry, distances and metrics between objects are of fundamental importance. Using a weaker notion than the classical distance, namely the weighted quasi-metrics, one can study the geometry of biological sequences (DNA, mRNA, or proteins) space. We analyze from the geometrical point of view a family of 60 insulin homologous sequences ranging on a large variety of living organisms from human to the nematode C. elegans. We show that the distances between sequences provide important information about the evolution and function of insulin.

Keywords: metric geometry, evolution, insulin, C. elegans

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Authors: L. K. Davis

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The effects of the evolution force are observable in nature at all structural levels ranging from small molecular systems to conversely enormous biospheric systems. However, the evolution force and work associated with formation of biological structures has yet to be described mathematically or theoretically. In addressing the conundrum, we consider evolution from a unique perspective and in doing so we introduce the “Fundamental Theory of the Evolution Force: FTEF”. We utilized synthetic evolution artificial intelligence (SYN-AI) to identify genomic building blocks and to engineer 14-3-3 ζ docking proteins by transforming gene sequences into time-based DNA codes derived from protein hierarchical structural levels. The aforementioned served as templates for random DNA hybridizations and genetic assembly. The application of hierarchical DNA codes allowed us to fast forward evolution, while dampening the effect of point mutations. Natural selection was performed at each hierarchical structural level and mutations screened using Blosum 80 mutation frequency-based algorithms. Notably, SYN-AI engineered a set of three architecturally conserved docking proteins that retained motion and vibrational dynamics of native Bos taurus 14-3-3 ζ.

Keywords: 14-3-3 docking genes, synthetic protein design, time-based DNA codes, writing DNA code from scratch

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Authors: Matthew T. Wilson

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This paper covers a selection of research utilizing grammar-based genetic programming, and illustrates how context-free grammar can be used to constrain genetic programming. It focuses heavily on grammatical evolution, one of the most popular variants of grammar-based genetic programming, and the way its operators and terminals are specialized and modified from those in genetic programming. A variety of implementations of grammatical evolution for general use are covered, as well as research each focused on using grammatical evolution or grammar-based genetic programming on a single application, or to solve a specific problem, including some of the classically considered genetic programming problems, such as the Santa Fe Trail.

Keywords: context-free grammar, genetic algorithms, genetic programming, grammatical evolution

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