Motivation: Long expansions of short tandem repeats (STRs), i.e. DNA repeats of 2–6 nt, are associated with some genetic diseases. Cost-efficient high-throughput sequencing can quickly produce billions of short reads that would be useful for uncovering disease-associated STRs. However, enumerating STRs in short reads remains largely unexplored because of the difficulty in elucidating STRs much longer than 100 bp, the typical length of short reads.Results: We propose ab initio procedures for sensing and locating long STRs promptly by using the frequency distribution of all STRs and paired-end read information. We validated the reproducibility of this method using biological replicates and used it to locate an STR associated with a brain disease (SCA31). Subsequently, we sequenced this STR site in 11 SCA31 samples using SMRTTM sequencing (Pacific Biosciences), determined 2.3–3.1 kb sequences at nucleotide resolution and revealed that (TGGAA)- and (TAAAATAGAA)-repeat expansions determined the instability of the repeat expansions associated with SCA31. Our method could also identify common STRs, (AAAG)- and (AAAAG)-repeat expansions, which are remarkably expanded at four positions in an SCA31 sample. This is the first proposed method for rapidly finding disease-associated long STRs in personal genomes using hybrid sequencing of short and long reads.Availability and implementation: Our TRhist software is available at http://trhist.gi.k.u-tokyo.ac.jp/.Contact: moris@cb.k.u-tokyo.ac.jpSupplementary information: Supplementary data are available at Bioinformatics online.

MANET (Mobile Ad-Hoc Network) is autonomous system, not based on existing infrastructure. Nodes usually change their position, network topology changes very fast. Service Based Routing is inherited from the model of Content Based Routing -CBR that manages and classifies many of network services. In order making nodes to communicate quickly and stablely, it requires applying some methodologies to reduce overhead and delay as well as power consumption. Therefore, this paper mentions a hierarchical clustered based routing using Tree.is a data structure with fast algorithms to establish, insert, update. It has been used in many fields effectively and efficiently such as Google Map, Forwarding technique, computer virtual memory. In combination with some artificial intelligence algorithms to make cluster, find optimized routes, multicast trees for effective communication. Fuzzy logic and genetic al. are proved to be very compatible with Manet. A genetic algorithm is used to choose optimized clusters, Fuzzy logic is applied to choose the cluster head and members of each cluster. Multiple paths routing is very importance for routing in MANET that making Quality of Service by Ant Colony Optimization Algorithm.

Abstract:In Cryptography, there are two kinds of methods for encryption and decryption. They are symmetric cryptography and asymmetric cryptography. In symmetric cryptography, it uses a single key for encryption and decryption. In asymmetric cryptography, it uses both public key and private key for encryption and decryption. In MANET (mobile ad-hoc network) every node usually moves and has limited energy, so network link is not stable and has low bandwidth. Therefore it is very carefully to choose the cryptography for ad-hoc network or MANET. If the transaction is very important, for example online banking, can use an asymmetric algorithm. So Elliptic Curve Cryptography is right choice. For data and control traffic, the symmetric cryptography can be the good selection, especially stream ciphers are very comfortable. We use Elliptic Curve Cryptography (ECC) with its arithmetic operations on finite fields to build public -key cryptographic schemes consisting of: i) signature schemes; ii) encryption schemes; and iii) key agreement schemes. In key management, public key cryptography is used to distribute the secret keys used in other cryptographic algorithms (for example DES). For digital signatures, public key cryptography is used to authenticate the origin of data and protect the integrity of that data. Early public key systems are secure based on difficulty of factoring a large integer composed by two or more large prime integers. With Elliptic Curve based protocol, its security is based on assuming that is difficult to find the discrete logarithm of a random point on Elliptic Curve with respect to a publicly known base point. The size of EC determines the level of difficulty of the problem. If comparing to RSA, with the same level of security, RSA has to use larger public key, for example ECC of 256 bits public key is with the same level of security as 3072 bits public key RSA. To use RSA or Diffie-Hellman to protect 128-bit AES keys one should use 3072-bit parameters: three times the size in use throughout the Internet today. The equivalent key size for elliptic curves is only 256 bits.

Abstract:In Service Based Routing (SBR), data is transmitted from a source node to destination nodes are not depended on destination addresses. Hence, it is comfortable with new advanced technology as cloud computing and also flexible and reliable. Genetic and Queen-Bee algorithms (GA, QB) are artificial intelligence techniques for combinatorial optimization problems solving based on some natural rules. In which GA is a branch of the evolutionary strategies that uses some principles of evolution theory, such as natural selection, mutation and crossover. QB is performed based on GA for energy saving. The tree is an effective data structure that can be used to organize a hierarchical clustering network with fast establishing, updating, tuning algorithms. The usage of the Greedy algorithm to find cyclic routes or multiple paths on each trunk by multiple criterions to transmit data effectively.

Mobile Ad-hoc Network (Manet) consists of a set of network nodes which change, not based on an existing network infrastructure as well as the centralized control. Network nodes usually have limited energy, bandwidth limitations, so find a way to transfer packets in the network is very important. To minimize packet loss, efficient bandwidth utilization at the node requires routing protocol must be compact, efficient, accurate. Fuzzy logic is a logical field studies evaluating the accuracy of the results based on the approximation of the components involved, make decisions based on many factors relative accuracy based on experimental or mathematical proof. Each component of the logical expression is usually belong to one set of defined unclear (fuzzy set). In this paper, We give some researchs applied fuzzy logic in assessing the network routing and bandwidth management on the basis of a number of existing studies.