Welcome to Journal of Theoretical and Applied Information Technology

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Compressing DNA sequences is an important task as every day thousands of gigabytes of sequences of nucleotides and amino acids gets stored in Genbank. Storing large Genomes in a personal computer in the compressed form is an efficient means of using DNA sequences for biological functions.
We present a compression algorithm, “HuffBit Compress” for DNA sequences based on a novel algorithm of assigning binary bit codes(0 and 1) for each base(A,C,G,T) to compress both repetitive and non repetitive DNA sequence. Our proposed algorithm achieves the compression ratio using the concept of Extended Binary Tree. In this algorithm Extended binary tree concept is applied to derieve a special class of variable-length codes that satisfy prefix property. This class of codes is called Huffman Codes. Huffman codes are based on relative frequency with which DNA symbols (A,C,G,T) appear in the sequence.
The specific bit sequence assigned to an individual base is determined by tracing out the path from the root of the tree to the leaf that represents that Base. By convention, bit '0' represents following the left child when tracing out the path and bit '1' represents following the right child when tracing out the path. The extended binary tree is constructed such that the paths from the root to the most frequently used bases are short while the paths to less frequently used bases are long. This results in short codes for frequently used bases and long codes for less frequently used bases.
If the sequences are encoded using the old trivial method of assigning 2 bits per base.(A=00,C=01,G=10,T=11) The encoded text is of higher length.(1000 bases needs 2000 bits of space). This proposed algorithm “HuffBit Compress” compresses DNA sequences more efficiently.(1000 bases may need only 1006 bits of space in Best case.). Analysis of Best case and worst case is defined for the first time in this Algorithm. Compression Ratio of 1.6 bits/base can be achieved using this proposed algorithm. This algorithm makes the near choice (minimum value) at every step that appears to lead to an overall optimal base encoding.

Huffman Codes, Compression Ratio, Internal Node, External Node, Extended Binary Tree, Encode, Decode

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This paper presents a new methodology using Particle Swarm Optimization(PSO) for the placement of Distributed Generators(DG) in the radial distribution systems to reduce the real power losses and to improve the voltage profile. A two-stage methodology is used for the optimal DG placement . In the first stage, single DG placement method is used to find the optimal DG locations and in the second stage, PSO is used to find the size of the DGs corresponding to maximum loss reduction. The proposed method is tested on standard IEEE 33 bus test system and the results are presented and compared with an existing method.

DG placement, fuzzy approach, PSO, loss reduction, radial distribution system

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We propose a Quality-of-Service (QoS)-based multicast routing protocol, referred to as QoS-MR, for mobile ad hoc networks (MANETs). QoS-MR is a receiver-initiated mesh-based multicast routing protocol and can work for both combinatorially stable and unstable networks. We explain in detail the procedures for mesh construction (initiation by the source, propagation of the control packets by the intermediate nodes and route selection by the receiver) and mesh maintenance/repair. We take into account QoS metrics such as bandwidth, end-to-end delay and link lifetime. The source specifies the desired QoS characteristics of the application in the control messages broadcast for mesh formation and the intermediate nodes forward the control messages only if they could satisfy the QoS demands and reserve the resources requested by the application. The receiver selects the route that best satisfies the QoS constraints and notifies the source. A congregate of all these source-receiver routes leads to the formation of a multicast mesh that also involves the links between the forwarding nodes of these routes. Mesh/route repair is conducted through an expanding ring search (ERS) approach to minimize the control overhead. An alternate route that best satisfies the QoS constraints is incorporated into the mesh.

Quality of Service, Multicast Routing Protocol, Mobile Ad hoc Networks, Link Expiration Time, Bandwidth, End-to-end Delay, Mesh

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This paper describes a maximum entropy named entity(Identifying and classifying personal, location, organization or other names) recognition system for Telugu language. Named entity (N.E) recognition is a form of information extraction in which we seek to classify every word in a document as being a person-name, organization name, location name, date or none of the above. Named entity recognition is an important task for many NLP applications.

Named Entity Recognition, Maximum Entropy, Named Entity, NLP,Telugu

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A new approach for fingerprint verification, based on wavelets and pseudo Zernike moments (PZMs), is discussed. PZMs are robust to noisy images, invariant to rotation and have a good image reconstruction capability [4]. PZMs have been used for global analysis and so they are used to extract global features (the shape of the fingerprint image). Wavelets are good at local analysis and so they help to extract local features (minutiae) from a fingerprint. Therefore, this hybrid approach extracts most significant features from the fingerprint images and achieve better verification rate. Different types of wavelets are used for the study but the result shows that Symmlet orthonormal wavelet of order 8 gives best verification rate.

Fingerprint Verification; Minutiae; Global Features; Local Features; Features Extraction; Wavelets Pseudo Zernike Moments

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In this paper we present an evaluation model for the chains of multimedia indexing tools that takes into consideration the user preferences in order to enable him to choose the most suitable chain of tools respecting his preferences.
Two approaches are proposed to extract indexing chains. The first one suggests building the whole graph for all indexes present in the platform. The second approach deal individually with each user request: only the corresponding sub-graph is built.

Automatic Multimedia Indexing, Evaluation model, Indexing Chain Approaches

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The minimum spanning tree clustering algorithm is capable of detecting clusters with irregular boundaries. In this paper we propose minimum spanning tree based clustering algorithm. The algorithm produces k clusters with Minimum Spanning Clustering Tree (MSCT), a new data structure which can be used as search tree. Our algorithm works in two phases. The first phase produces subtree (cluster). The second phase converts the subtree into binary tree called MSCT.

Minimum Spanning Clustering trees, Euclidean Minimum Spanning Tree, Clusters, Subtree

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This paper presents an improved Particle Swarm Optimization (PSO) algorithm for solving Transient Stability Constrained Optimal Power Flow (TSCOPF) problem through the application of Gaussian and Cauchy probability distributions. The modified PSO approach introduces new diversification and intensification strategy into the particles thus preventing PSO algorithm from premature convergence. The controllable system quantities are optimized to minimize fuel cost of the power generation. An IEEE 30-bus test system is taken for investigation. The transient stability constrained optimal power flow results obtained using the improved PSO models are compared with those obtained using standard PSO and GA algorithms. The investigations reveal that the proposed algorithm is relatively simple, reliable and efficient and suitable for on-line applications.

Optimal power flow, Transient stability, Particle swarm optimization, Gaussian probability distribution function, Cauchy probability distribution function

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The Transmission Control Protocol (TCP) is the most popular transport layer protocol for the internet. Congestion Control is used to increase the congestion window size if there is additional bandwidth on the network, and decrease the congestion window size when there is congestion.
This paper uses a classic TCP which we called Robust TCP with an accurate algorithm of congestion detection in order to improve the performance of TCP. Our TCP Robust only reacts when it receives an ECN (Explicit Congestion Notification) mark. The evaluation result shows a good performance in the terms of drop ratio and throughput.

Congestion Control, TCP, ECN, Implicit Congestion Notification

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The purpose of this paper is to study the Bose, Chaudhuri, and Hocquenghem (BCH) code, with an aim to simulate the encoding and decoding processes. The gain of the proposed code in investigated through applying it to binary phase sift keying (BPSK) modulation scheme in symmetric additive white Gaussian noise (AWGN) channel. The bit error probability (BEP) of coded (63, 36) BCH system was evaluated and compared with the performance of un-coded system.

Performance Analysis, Chaudhuri, And Hocquenghem (BCH) Code, Binary Phase Sift Keyin, Bit Error Probability, Additive White Gaussian Noise