Families of sequences with good family complexity and cross-correlation measure

In this paper we study pseudorandomness of a family of sequences in terms of two measures, the family complexity ($f$-complexity) and the cross-correlation measure of order $\ell$. We consider sequences not only on binary alphabet but also on $k$-symbols ($k$-ary) alphabet. We first generalize some known methods on construction of the family of binary pseudorandom sequences. We prove a bound on the $f$-complexity of a large family of binary sequences of Legendre-symbols of certain irreducible polynomials. We show that this family as well as its dual family have both a large family complexity and a small cross-correlation measure up to a rather large order. Next, we present another family of binary sequences having high $f$-complexity and low cross-correlation measure. Then we extend the results to the family of sequences on $k$-symbols alphabet.Comment: 13 pages. Comments are welcome

A Family of Binary Sequences with Optimal Correlation Property and Large Linear Span

A family of binary sequences is presented and proved to have optimal correlation property and large linear span. It includes the small set of Kasami sequences, No sequence set and TN sequence set as special cases. An explicit lower bound expression on the linear span of sequences in the family is given. With suitable choices of parameters, it is proved that the family has exponentially larger linear spans than both No sequences and TN sequences. A class of ideal autocorrelation sequences is also constructed and proved to have large linear span.Comment: 21 page

High-rate self-synchronizing codes

Self-synchronization under the presence of additive noise can be achieved by allocating a certain number of bits of each codeword as markers for synchronization. Difference systems of sets are combinatorial designs which specify the positions of synchronization markers in codewords in such a way that the resulting error-tolerant self-synchronizing codes may be realized as cosets of linear codes. Ideally, difference systems of sets should sacrifice as few bits as possible for a given code length, alphabet size, and error-tolerance capability. However, it seems difficult to attain optimality with respect to known bounds when the noise level is relatively low. In fact, the majority of known optimal difference systems of sets are for exceptionally noisy channels, requiring a substantial amount of bits for synchronization. To address this problem, we present constructions for difference systems of sets that allow for higher information rates while sacrificing optimality to only a small extent. Our constructions utilize optimal difference systems of sets as ingredients and, when applied carefully, generate asymptotically optimal ones with higher information rates. We also give direct constructions for optimal difference systems of sets with high information rates and error-tolerance that generate binary and ternary self-synchronizing codes.Comment: 9 pages, no figure, 2 tables. Final accepted version for publication in the IEEE Transactions on Information Theory. Material presented in part at the International Symposium on Information Theory and its Applications, Honolulu, HI USA, October 201

Computational identification and analysis of noncoding RNAs - Unearthing the buried treasures in the genome

The central dogma of molecular biology states that the genetic information flows from DNA to RNA to protein. This dogma has exerted a substantial influence on our understanding of the genetic activities in the cells. Under this influence, the prevailing assumption until the recent past was that genes are basically repositories for protein coding information, and proteins are responsible for most of the important biological functions in all cells. In the meanwhile, the importance of RNAs has remained rather obscure, and RNA was mainly viewed as a passive intermediary that bridges the gap between DNA and protein. Except for classic examples such as tRNAs (transfer RNAs) and rRNAs (ribosomal RNAs), functional noncoding RNAs were considered to be rare. However, this view has experienced a dramatic change during the last decade, as systematic screening of various genomes identified myriads of noncoding RNAs (ncRNAs), which are RNA molecules that function without being translated into proteins [11], [40]. It has been realized that many ncRNAs play important roles in various biological processes. As RNAs can interact with other RNAs and DNAs in a sequence-specific manner, they are especially useful in tasks that require highly specific nucleotide recognition [11]. Good examples are the miRNAs (microRNAs) that regulate gene expression by targeting mRNAs (messenger RNAs) [4], [20], and the siRNAs (small interfering RNAs) that take part in the RNAi (RNA interference) pathways for gene silencing [29], [30]. Recent developments show that ncRNAs are extensively involved in many gene regulatory mechanisms [14], [17]. The roles of ncRNAs known to this day are truly diverse. These include transcription and translation control, chromosome replication, RNA processing and modification, and protein degradation and translocation [40], just to name a few. These days, it is even claimed that ncRNAs dominate the genomic output of the higher organisms such as mammals, and it is being suggested that the greater portion of their genome (which does not encode proteins) is dedicated to the control and regulation of cell development [27]. As more and more evidence piles up, greater attention is paid to ncRNAs, which have been neglected for a long time. Researchers began to realize that the vast majority of the genome that was regarded as “junk,” mainly because it was not well understood, may indeed hold the key for the best kept secrets in life, such as the mechanism of alternative splicing, the control of epigenetic variations and so forth [27]. The complete range and extent of the role of ncRNAs are not so obvious at this point, but it is certain that a comprehensive understanding of cellular processes is not possible without understanding the functions of ncRNAs [47]

Design of One-Coincidence Frequency Hopping Sequence Sets for FHMA Systems

Department of Electrical EngineeringIn the thesis, we discuss frequency hopping multiple access (FHMA) systems and construction of optimal frequency hopping sequence and applications. Moreover, FHMA is widely used in modern communication systems such as Bluetooth, ultrawideband (UWB), military, etc. For these systems, it is desirable to employ frequency-hopping sequences (FHSs) having low Hamming correlation in order to reduce the multiple-access interference. In general, optimal FHSs with respect to the Lempel-Greenberger bound do not always exist for all lengths and frequency set sizes. Therefore, it is an important problem to verify whether an optimal FHS with respect to the Lempel-Greenberger bound exists or not for a given length and a given frequency set size. I constructed FHS satisfying optimal with respect to the Lempel-Greenberger bound and Peng-Fan bound for efficiency of available frequency. Parameters of a new OC-FHS set are length p^2-p over Z_(p^2 ) by using a primitive element of Z_p. The new OC-FHS set with H_a (X)=0 and H_c (X)=1 can be applied to several recent applications using ISM band (e.g. IoT) based on BLE and Zigbee. In the construction and theorem, I used these mathematical back grounds in preliminaries (i.e., finite field, primitive element, primitive polynomial, frequency hopping sequence, multiple frequency shift keying, DS/CDMA) in order to prove mathematically. The outline of thesis is as follows. In preliminaries, we explain algorithm for minimal polynomial for sequence, linear complexities, Hamming correlation and bounds for FHSs and some applications are presented. In section ???, algorithm for complexity, correlation and bound for FHSs and some applications are presented. In section ???, using information in section ??? and ???, a new construction of OC-FHS is presented. In order to prove the optimality of FHSs, all cases of Hamming autocorrelation and Hamming cross-correlation are mathematically calculated. Moreover, in order to raise data rate or the number of users, a new method is presented. Using this method, sequences are divided into two times of length and satisfies Lempel-Greenberger bound and Peng-Fan bound.clos