**Commenced**in January 2007

**Frequency:**Monthly

**Edition:**International

**Paper Count:**1297

# Search results for: negative sequence

##### 1297 Multiple Sequence Alignment Using Optimization Algorithms

**Authors:**
M. F. Omar,
R. A. Salam,
R. Abdullah,
N. A. Rashid

**Abstract:**

Proteins or genes that have similar sequences are likely to perform the same function. One of the most widely used techniques for sequence comparison is sequence alignment. Sequence alignment allows mismatches and insertion/deletion, which represents biological mutations. Sequence alignment is usually performed only on two sequences. Multiple sequence alignment, is a natural extension of two-sequence alignment. In multiple sequence alignment, the emphasis is to find optimal alignment for a group of sequences. Several applicable techniques were observed in this research, from traditional method such as dynamic programming to the extend of widely used stochastic optimization method such as Genetic Algorithms (GAs) and Simulated Annealing. A framework with combination of Genetic Algorithm and Simulated Annealing is presented to solve Multiple Sequence Alignment problem. The Genetic Algorithm phase will try to find new region of solution while Simulated Annealing can be considered as an alignment improver for any near optimal solution produced by GAs.

**Keywords:**
Simulated annealing,
genetic algorithm,
sequence alignment,
multiple sequence alignment.

##### 1296 Fractal Analysis of 16S rRNA Gene Sequences in Archaea Thermophiles

**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

##### 1295 An Approach in the Improvement of the Reliability of Impedance Relay

**Authors:**
D. Ouahdi,
R. Ladjeroud,
I. Habi

**Abstract:**

The distance protection mainly the impedance relay which is considered as the main protection for transmission lines can be subjected to impedance measurement error which is, mainly, due to the fault resistance and to the power fluctuation. Thus, the impedance relay may not operate for a short circuit at the far end of the protected line (case of the under reach) or operates for a fault beyond its protected zone (case of overreach). In this paper, an approach to fault detection by a distance protection, which distinguishes between the faulty conditions and the effect of overload operation mode, has been developed. This approach is based on the symmetrical components; mainly the negative sequence, and it is taking into account both the effect of fault resistance and the overload situation which both have an effect upon the reliability of the protection in terms of dependability for the former and security for the latter.

**Keywords:**
Distance Protection,
Fault Detection,
negative
sequence,
overload,
Transmission line.

##### 1294 Parallezation Protein Sequence Similarity Algorithms using Remote Method Interface

**Authors:**
Mubarak Saif Mohsen,
Zurinahni Zainol,
Rosalina Abdul Salam,
Wahidah Husain

**Abstract:**

One of the major problems in genomic field is to perform sequence comparison on DNA and protein sequences. Executing sequence comparison on the DNA and protein data is a computationally intensive task. Sequence comparison is the basic step for all algorithms in protein sequences similarity. Parallel computing is an attractive solution to provide the computational power needed to speedup the lengthy process of the sequence comparison. Our main research is to enhance the protein sequence algorithm using dynamic programming method. In our approach, we parallelize the dynamic programming algorithm using multithreaded program to perform the sequence comparison and also developed a distributed protein database among many PCs using Remote Method Interface (RMI). As a result, we showed how different sizes of protein sequences data and computation of scoring matrix of these protein sequence on different number of processors affected the processing time and speed, as oppose to sequential processing.

**Keywords:**
Protein sequence algorithm,
dynamic programming algorithm,
multithread

##### 1293 Software Evolution Based Sequence Diagrams Merging

**Authors:**
Zine-Eddine Bouras,
Abdelouaheb Talai

**Abstract:**

**Keywords:**
System behaviors,
sequence diagram merging,
dependence analysis,
sequence diagram slicing.

##### 1292 A New Class F2 (M, 0, N)L„ p)F of The Double Difference Sequences of Fuzzy Numbers

**Authors:**
N. Subramanian,
C. Murugesan

**Abstract:**

The double difference sequence space I2 (M, of fuzzy numbers for both 1 < p < oo and 0 < p < 1, is introduced. Some general properties of this sequence space are studied. Some inclusion relations involving this sequence space are obtained.

**Keywords:**
Orlicz function,
solid space,
metric space,
completeness

##### 1291 An Improved Fast Search Method Using Histogram Features for DNA Sequence Database

**Authors:**
Qiu Chen,
Feifei Lee,
Koji Kotani,
Tadahiro Ohmi

**Abstract:**

**Keywords:**
Fast search,
DNA sequence,
Histogram feature,
Smith-Waterman algorithm,
Local search

##### 1290 Identifying New Sequence Features for Exon-Intron Discrimination by Rescaled-Range Frameshift Analysis

**Authors:**
Sing-Wu Liou,
Yin-Fu Huang

**Abstract:**

**Keywords:**
Exon-Intron Discrimination,
Rescaled-Range Frameshift Analysis,
Frameshift Sensitivity,
Accumulative Sequence Complexity

##### 1289 Interactive Model Based On an Extended CPN

**Authors:**
Shuzhen Yao,
Fengjing Zhao,
Jianwei He

**Abstract:**

The UML modeling of complex distributed systems often is a great challenge due to the large amount of parallel real-time operating components. In this paper the problems of verification of such systems are discussed. ECPN, an Extended Colored Petri Net is defined to formally describe state transitions of components and interactions among components. The relationship between sequence diagrams and Free Choice Petri Nets is investigated. Free Choice Petri Net theory helps verifying the liveness of sequence diagrams. By converting sequence diagrams to ECPNs and then comparing behaviors of sequence diagram ECPNs and statecharts, the consistency among models is analyzed. Finally, a verification process for an example model is demonstrated.

**Keywords:**
Consistency,
liveness,
Petri Net,
sequence diagram.

##### 1288 Optimization of Supersonic Ejector via Sequence-Adapted Micro-Genetic Algorithm

**Authors:**
Kolar Jan,
Dvorak Vaclav

**Abstract:**

In this study, an optimization of supersonic air-to-air ejector is carried out by a recently developed single-objective genetic algorithm based on adaption of sequence of individuals. Adaptation of sequence is based on Shape-based distance of individuals and embedded micro-genetic algorithm. The optimal sequence found defines the succession of CFD-aimed objective calculation within each generation of regular micro-genetic algorithm. A spring-based deformation mutates the computational grid starting the initial individualvia adapted population in the optimized sequence. Selection of a generation initial individual is knowledge-based. A direct comparison of the newly defined and standard micro-genetic algorithm is carried out for supersonic air-to-air ejector. The only objective is to minimize the loose of total stagnation pressure in the ejector. The result is that sequence-adopted micro-genetic algorithm can provide comparative results to standard algorithm but in significantly lower number of overall CFD iteration steps.

**Keywords:**
Grid deformation,
Micro-genetic algorithm,
shapebased
sequence,
supersonic ejector.

##### 1287 Sequence Relationships Similarity of Swine Influenza a (H1N1) Virus

**Authors:**
Patsaraporn Somboonsak,
Mud-Armeen Munlin

**Abstract:**

**Keywords:**
Sequence DNA,
Relationship of swine,
Swineinfluenza,
Sequence Similarity

##### 1286 On Some Subspaces of Entire Sequence Space of Fuzzy Numbers

**Authors:**
T. Balasubramanian,
A. Pandiarani

**Abstract:**

In this paper we introduce some subspaces of fuzzy entire sequence space. Some general properties of these sequence spaces are discussed. Also some inclusion relation involving the spaces are obtained. Mathematics Subject Classification: 40A05, 40D25.

**Keywords:**
Fuzzy Numbers,
Entire sequences,
completeness,
Fuzzy entire sequences

##### 1285 The Economic Lot Scheduling Problem in Flow Lines with Sequence-Dependent Setups

**Authors:**
M. Heydari,
S. A. Torabi

**Abstract:**

**Keywords:**
Economic lot scheduling problem,
finite horizon,
genetic algorithm,
mixed zero-one nonlinear programming,
sequence-dependent.

##### 1284 Symbolic Model Checking of Interactions in Sequence Diagrams with Combined Fragments by SMV

**Authors:**
Yuka Kawakami,
Tomoyuki Yokogawa,
Hisashi Miyazaki,
Sousuke Amasaki,
Yoichiro Sato,
Michiyoshi Hayase

**Abstract:**

In this paper, we proposed a method for detecting consistency violation between state machine diagrams and a sequence diagram defined in UML 2.0 using SMV. We extended a method expressing these diagrams defined in UML 1.0 with boolean formulas so that it can express a sequence diagram with combined fragments introduced in UML 2.0. This extension made it possible to represent three types of combined fragment: alternative, option and parallel. As a result of experiment, we confirmed that the proposed method could detect consistency violation correctly with SMV.

**Keywords:**
UML,
model checking,
SMV,
sequence diagram.

##### 1283 On the Central Limit Theorems for Forward and Backward Martingales

**Authors:**
Yilun Shang

**Abstract:**

**Keywords:**
central limit theorem,
martingale difference sequence,
backward martingale.

##### 1282 Computer Aided Assembly Attributes Retrieval Methods for Automated Assembly Sequence Generation

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

**Abstract:**

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 sequence generation,
computer aided design.

##### 1281 Predicting Protein Function using Decision Tree

**Authors:**
Manpreet Singh,
Parminder Kaur Wadhwa,
Surinder Kaur

**Abstract:**

**Keywords:**
Sequence Derived Features,
decision tree.

##### 1280 M-ary Chaotic Sequence Based SLM-OFDM System for PAPR Reduction without Side-Information

**Authors:**
A.Goel,
M. Agrawal,
P. Gupta Poddar

**Abstract:**

Selected Mapping (SLM) is a PAPR reduction technique, which converts the OFDM signal into several independent signals by multiplication with the phase sequence set and transmits one of the signals with lowest PAPR. But it requires the index of the selected signal i.e. side information (SI) to be transmitted with each OFDM symbol. The PAPR reduction capability of the SLM scheme depends on the selection of phase sequence set. In this paper, we have proposed a new phase sequence set generation scheme based on M-ary chaotic sequence and a mapping scheme to map quaternary data to concentric circle constellation (CCC) is used. It is shown that this method does not require SI and provides better SER performance with good PAPR reduction capability as compared to existing SLMOFDM methods.

**Keywords:**
Orthogonal frequency division multiplexing
(OFDM),
Peak-to-average power ratio (PAPR),
Selected mapping
(SLM),
Side information (SI)

##### 1279 Multicasting Characteristics of All-Optical Triode Based On Negative Feedback Semiconductor Optical Amplifiers

**Authors:**
S. Aisyah Azizan,
M. Syafiq Azmi,
Yuki Harada,
Yoshinobu Maeda,
Takaomi Matsutani

**Abstract:**

We introduced an all-optical multicasting characteristics with wavelength conversion based on a novel all-optical triode using negative feedback semiconductor optical amplifier. This study was demonstrated with a transfer speed of 10 Gb/s to a non-return zero 231-1 pseudorandom bit sequence system. This multi-wavelength converter device can simultaneously provide three channels of output signal with the support of non-inverted and inverted conversion. We studied that an all-optical multicasting and wavelength conversion accomplishing cross gain modulation is effective in a semiconductor optical amplifier which is effective to provide an inverted conversion thus negative feedback. The relationship of received power of back to back signal and output signals with wavelength 1535 nm, 1540 nm, 1545 nm, 1550 nm, and 1555 nm with bit error rate was investigated. It was reported that the output signal wavelengths were successfully converted and modulated with a power penalty of less than 8.7 dB, which the highest is 8.6 dB while the lowest is 4.4 dB. It was proved that all-optical multicasting and wavelength conversion using an optical triode with a negative feedback by three channels at the same time at a speed of 10 Gb/s is a promising device for the new wavelength conversion technology.

**Keywords:**
Cross gain modulation,
multicasting,
negative
feedback optical amplifier,
semiconductor optical amplifier.

##### 1278 On the Properties of Pseudo Noise Sequences with a Simple Proposal of Randomness Test

**Authors:**
Abhijit Mitra

**Abstract:**

**Keywords:**
Maximal length sequence,
pseudo noise sequence,
punctured de Bruijn sequence,
auto-correlation,
Bernoulli sequence,
randomness tests.

##### 1277 Power Efficient OFDM Signals with Reduced Symbol's Aperiodic Autocorrelation

**Authors:**
Ibrahim M. Hussain

**Abstract:**

Three new algorithms based on minimization of autocorrelation of transmitted symbols and the SLM approach which are computationally less demanding have been proposed. In the first algorithm, autocorrelation of complex data sequence is minimized to a value of 1 that results in reduction of PAPR. Second algorithm generates multiple random sequences from the sequence generated in the first algorithm with same value of autocorrelation i.e. 1. Out of these, the sequence with minimum PAPR is transmitted. Third algorithm is an extension of the second algorithm and requires minimum side information to be transmitted. Multiple sequences are generated by modifying a fixed number of complex numbers in an OFDM data sequence using only one factor. The multiple sequences represent the same data sequence and the one giving minimum PAPR is transmitted. Simulation results for a 256 subcarrier OFDM system show that significant reduction in PAPR is achieved using the proposed algorithms.

**Keywords:**
Aperiodic autocorrelation,
OFDM,
PAPR,
SLM,
wireless communication.

##### 1276 Pilot Directional Protection Scheme Using Wireless Communication

**Authors:**
Nitish Sharma,
G. G. Karady

**Abstract:**

**Keywords:**
Smart grid protection,
pilot protection,
power system simulation,
wireless communication.

##### 1275 Metal Berthelot Tubes with Windows for Observing Cavitation under Static Negative Pressure

**Authors:**
K. Hiro,
Y. Imai,
T. Sasayama

**Abstract:**

Cavitation under static negative pressure is not revealed well. The Berthelot method to generate such negative pressure can be a means to study cavitation inception. In this study, metal Berthelot tubes built in observation windows are newly developed and are checked whether high static negative pressure is generated or not. Negative pressure in the tube with a pair of a corundum plate and an aluminum gasket increased with temperature cycles. The trend was similar to that as reported before.

**Keywords:**
Berthelot method,
negative pressure,
cavitation.

##### 1274 UTMGO: A Tool for Searching a Group of Semantically Related Gene Ontology Terms and Application to Annotation of Anonymous Protein Sequence

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

**Abstract:**

**Keywords:**
Anonymous protein sequence,
Gene Ontology,
Protein sequence annotation,
Protein sequence alignment

##### 1273 Evaluation of the Zero Sequence Impedance of Overhead High Voltage Lines

**Authors:**
Rabah Diabi

**Abstract:**

**Keywords:**
Overhead line,
power system,
zero sequence,
wire guard,
grounding.

##### 1272 A Green Design for Assembly Model for Integrated Design Evaluation and Assembly and Disassembly Sequence Planning

**Authors:**
Yuan-Jye Tseng,
Fang-Yu Yu,
Feng-Yi Huang

**Abstract:**

**Keywords:**
green design,
assembly and disassembly sequence
planning,
green design for assembly,
particle swarm optimization.

##### 1271 A PN Sequence Generator based on Residue Arithmetic for Multi-User DS-CDMA Applications

**Authors:**
Chithra R,
Pallab Maji,
Sarat Kumar Patra,
Girija Sankar Rath

**Abstract:**

**Keywords:**
Direct-Sequence Code Division Multiple Access (DSCDMA),
Multiple-Access Interference (MAI),
PN Sequence,
Residue
Number System (RNS).

##### 1270 Moment Estimators of the Parameters of Zero-One Inflated Negative Binomial Distribution

**Authors:**
Rafid Saeed Abdulrazak Alshkaki

**Abstract:**

**Keywords:**
Zero one inflated models,
negative binomial distribution,
moments estimator,
non-negative integer sampling.

##### 1269 A Note on Negative Hypergeometric Distribution and Its Approximation

**Authors:**
S. B. Mansuri

**Abstract:**

**Keywords:**
Negative hypergeometric distribution,
Poisson distribution,
Poisson approximation,
Stein-Chen identity,
w-function.

##### 1268 Learning to Recommend with Negative Ratings Based on Factorization Machine

**Authors:**
Caihong Sun,
Xizi Zhang

**Abstract:**

Rating prediction is an important problem for recommender systems. The task is to predict the rating for an item that a user would give. Most of the existing algorithms for the task ignore the effect of negative ratings rated by users on items, but the negative ratings have a significant impact on users’ purchasing decisions in practice. In this paper, we present a rating prediction algorithm based on factorization machines that consider the effect of negative ratings inspired by Loss Aversion theory. The aim of this paper is to develop a concave and a convex negative disgust function to evaluate the negative ratings respectively. Experiments are conducted on MovieLens dataset. The experimental results demonstrate the effectiveness of the proposed methods by comparing with other four the state-of-the-art approaches. The negative ratings showed much importance in the accuracy of ratings predictions.

**Keywords:**
Factorization machines,
feature engineering,
negative ratings,
recommendation systems.