The assembly of a multiple sequence alignment (MSA) has become one of the most common tasks when dealing with sequence analysis. Unfortunately, the wide range of available methods and the differences in the results given by these methods makes it hard for a non-specialist to decide which program is best suited for a given purpose. In this review we briefly describe existing techniques and expose the potential strengths and weaknesses of the most widely used multiple alignment packages.

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Recent progress in multiple sequence alignment: a survey.

Trust mechanisms in wireless sensor networks: Attack analysis and countermeasures

In this paper, we propose a human-based model which builds a trust relationship between nodes in an ad hoc network. The trust is based on previous individual experiences and on the recommendations of others. We present the Recommendation Exchange Protocol (REP) which allows nodes to exchange recommendations about their neighbors. Our proposal does not require disseminating the trust information over the entire network. Instead, nodes only need to keep and exchange trust information about nodes within the radio range. Without the need for a global trust knowledge, our proposal scales well for large networks while still reducing the number of exchanged messages and therefore the energy consumption. In addition, we mitigate the effect of colluding attacks composed of liars in the network. A key concept we introduce is the relationship maturity, which allows nodes to improve the efficiency of the proposed model for mobile scenarios. We show the correctness of our model in a single-hop network through simulations. We also extend the analysis to mobile multihop networks, showing the benefits of the maturity relationship concept. We evaluate the impact of malicious nodes that send false recommendations to degrade the efficiency of the trust model. At last, we analyze the performance of the REP protocol and show its scalability. We show that our implementation of REP can significantly reduce the number messages.

Trust management in mobile ad hoc networks using a scalable maturity-based model

Trust evaluation plays an important role in securing wireless sensor networks (WSNs), which is one of the most popular network technologies for the Internet of Things (IoT). The efficiency of the trust evaluation process is largely governed by the trust derivation, as it dominates the overhead in the process, and performance of WSNs is particularly sensitive to overhead due to the limited bandwidth and power. This paper proposes an energy-aware trust derivation scheme using game theoretic approach, which manages overhead while maintaining adequate security of WSNs. A risk strategy model is first presented to stimulate WSN nodes’ cooperation. Then, a game theoretic approach is applied to the trust derivation process to reduce the overhead of the process. We show with the help of simulations that our trust derivation scheme can achieve both intended security and high efficiency suitable for WSN-based IoT networks.

An Energy-Aware Trust Derivation Scheme With Game Theoretic Approach in Wireless Sensor Networks for IoT Applications

Multipath routing can reduce the need for route updates, balance the traffic load and increase the data transfer rate in a wireless sensor network, improving the utilization of the limited energy of sensor nodes. However, previous multiple path routing methods use flooding for route discovery and transmit data with maximum power regardless of need, which results in waste of energy. Moreover, often a serious problem of collisions among multiple paths arises. In this paper, we propose an energy efficient and collision aware (EECA) node-disjoint multipath routing algorithm for wireless sensor networks. With the aid of node position information, the EECA algorithm attempts to find two collision-free routes using constrained and power adjusted flooding and then transmits the data with minimum power needed through power control component of the protocol. Our preliminary simulation results show that ECCA algorithm results in good overall performance, saving energy and transferring data efficiently.

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Energy Efficient Collision Aware Multipath Routing for Wireless Sensor Networks

As wireless sensor networks (WSNs) are widely used in unattended environments, various physical attacks are occurred easily In this paper, location and trust based replica detection (LTBRD) method is introduced to identify the replication attack in the wireless sensor network As sensor nodes are not tamper proof, all the credentials can be copied into any number of nodes In order to solve this issue, behavior based and certificate based trust along with location information is followed in our proposed LTBRD approach Depending upon the location mismatch and the trust value the malicious node will be identified and it will be revoked from the network In this approach, the efficiency of the algorithm is been achieved by aggregation as well as without aggregation The performance of LTBRD is evaluated with the help of detection probability, energy consumption, network delay, memory requirement The performance of LTBRD is proven theoretically and the result shows that the proposed algorithm outperforms well when compared with the existing algorithms such as RED and LSM

Distributed Location and Trust Based Replica Detection in Wireless Sensor Networks

Trust-based evolutionary game model assisting AODV routing against selfishness

Mobile Ad hoc Networks are characterized by multi-hop wireless links, without any infrastructure, and frequent host mobility A plethora of routing protocols has been proposed A class of routing protocols called on-demand protocols has recently gained attention because of their efficiency and low routing overhead As the mobile nodes in the network work on low power batteries, the need to take into account their power consumption arises This paper focuses on a particular on-demand routing protocol, called Dynamic Source Routing, and shows how an efficient heuristic based Multipath technique can improve the mean time to node failure and maintain the variance in the power of all the nodes as low as possible In the Multipath Power Sensitive Routing Protocol (MPSR) every node in the network is treated equally and the overall network is stable for a long time An interesting feature of using this protocol is that the end-to-end packet delay does not increase significantly The results of extensive simulation show that the performance of MPSR protocol is on an increasing trend as mobility increases when compared to the Dynamic Source Routing

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Multipath Power Sensitive Routing Protocol for Mobile Ad Hoc Networks

†‡ This paper presents an evolution-bas ed approach for solving multiple molecular sequence alignment. The approach is based on the island parallel genetic algorithm that relies on the fitness distribution over the population of alig nments. The algorithm searches for an alignment among the independent isolated evolving populations by optimizing weighted sum of pairs objective function which measures the alignment quality. The parallel approach is impl emented on PARAM 10000, a parallel machine developed at the Center for Development of Advanced Computing, Pune, and is shown to consistently perform better than the sequential genetic algorithm. The algorithm yields alignments that are qualitatively better than an alternative method, ClustalW.

Multiple molecular sequence alignment by island parallel genetic algorithm

An efficient approach to solve multiple sequence alignment problem is presented in this paper. This approach is based on parallel genetic algorithm(PGA) that runs on a networked parallel environment. The algorithm optimizes an objective function 'weighted sums of pairs' which measures alignment quality. Using isolated independent subpopulations of alignments in a quasi evolutionary manner this approach gradually improves the fitness of the subpopulations as measured by an objective function. This parallel approach is shown to perform better than the sequential approach and an alternative method, clustalw. An investigation of the parameters of the algorithm further confirms the better performance.

P. Narayanasamy

Papers

Distributed Location and Trust Based Replica Detection in Wireless Sensor Networks

Trust-based evolutionary game model assisting AODV routing against selfishness

Multipath Power Sensitive Routing Protocol for Mobile Ad Hoc Networks

Multiple molecular sequence alignment by island parallel genetic algorithm

Multiple Sequence Alignment Using Parallel Genetic Algorithms