• Bioinformatics and Biosystems
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• v.1 no.1
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• pp.46-50
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• 2006

According to the advancement of experimental techniques in molecular biology, genomic and protein sequence databases are increasing in size exponentially, and mean sequence lengths are also increasing. Because the sizes of these databases become larger, it is difficult to search similar sequences in biological databases with significant homologies to a query sequence. In this paper, we present the N-gram indexing method to retrieve similar sequences fast, precisely and comparably. This method regards a protein sequence as a text written in language of 20 amino acid codes, adapts N-gram tokens of fixed-length as its indexing scheme for sequence strings. After such tokens are indexed for all the sequences in the database, sequences can be searched with information retrieval algorithms. Using this new method, we have developed a protein sequence search system named as ProSeS (PROtein Sequence Search). ProSeS is a protein sequence analysis system which provides overall analysis results such as similar sequences with significant homologies, predicted subcellular locations of the query sequence, and major keywords extracted from annotations of similar sequences. We show experimentally that the N-gram indexing approach saves the retrieval time significantly, and that it is as accurate as current popular search tool BLAST.

• Korean Journal of Computational Design and Engineering
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• v.6 no.4
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• pp.244-253
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• 2001

For more complete process planning, machining sequence determination is critical to attain machining economics. Although many studies have been conducted in recent years, most of them suggests the non-unique machining sequences. When the tool approach directions(TAD) are considered fur a feature, both machining time and number of setups can be reduced. Then, the unique machining sequence can be extracted from alternate(non-unique) sequences by minimizing the idle time between operations within a sequence. This study develops an algorithm to generate the best machining sequence for composite prismatic features in a vertical milling operation. The algorithm contains five steps to produce an unique sequence: a precedence relation matrix(PRM) development, tool approach direction determination, machining time calculation, alternate machining sequence generation, and finally, best machining sequence generation with idle times. As a result, the study shows that the algorithm is effective for a given composite feature and can be applicable fur other prismatic parts.

• Journal of information and communication convergence engineering
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• v.16 no.3
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• pp.166-172
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• 2018

A pseudo-random sequence generated by using a primitive polynomial, trace function, and Legendre symbol has been researched in our previous work. Our previous sequence has some interesting features such as period, autocorrelation, and linear complexity. A pseudo-random sequence widely used in cryptography. However, from the aspect of the practical use in cryptographic systems sequence needs to generate swiftly. Our previous sequence generated by utilizing a primitive polynomial, however, finding a primitive polynomial requires high calculating cost when the degree or the characteristic is large. It’s a shortcoming of our previous work. The main contribution of this work is to find some relation between the generated sequence and irreducible polynomials. The purpose of this relationship is to generate the same sequence without utilizing a primitive polynomial. From the experimental observation, it is found that there are (p - 1)/2 kinds of polynomial, which generates the same sequence. In addition, some of these polynomials are non-primitive polynomial. In this paper, these relationships between the sequence and the polynomials are shown by some examples. Furthermore, these relationships are proven theoretically also.

• Journal of Communications and Networks
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• v.14 no.3
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• pp.230-236
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• 2012

Based on the known binary sequence sets and Gray mapping, a new method for constructing quaternary sequence sets is presented and the resulting sequence sets' properties are investigated. As three direct applications of the proposed method, when we choose the binary aperiodic, periodic, and Z-complementary sequence sets as the known binary sequence sets, the resultant quaternary sequence sets are the quaternary aperiodic, periodic, and Z-complementary sequence sets, respectively. In comparison with themethod proposed by Jang et al., the new method can cope with either both the aperiodic and periodic cases or both even and odd lengths of sub-sequences, whereas the former is only fit for the periodic case with even length of sub-sequences. As a consequence, by both our and Jang et al.'s methods, an arbitrary binary aperiodic, periodic, or Z-complementary sequence set can be transformed into a quaternary one no matter its length of sub-sequences is odd or even. Finally, a table on the existing quaternary periodic complementary sequence sets is given as well.

• Journal of Integrative Natural Science
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• v.1 no.3
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• pp.230-233
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• 2008

A simple and rapid method is described for extending the 5'- or 3'-end genomic sequence of a known partial sequence by only a single round of PCR. This method involves digesting and ligating genomic and plasmid DNAs, and amplifying the 5'-upstream or 3'-end downstream sequence of the known DNA sequence, using two primers, one gene specific and the other plasmid specific. A single round of PCR amplification is sufficient to produce gene-specific bands detectable in gels. By using this approach, 5'-end genomic sequence of the D-amoeba sams gene was extended.

• Genomics & Informatics
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• v.4 no.4
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• pp.173-181
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• 2006

Pattern finding is one of the important tasks in a protein or DNA sequence analysis. Alignment is the widely used technique for finding patterns in sequence analysis. BLAST (Basic Local Alignment Search Tool) is one of the most popularly used tools in bio-informatics to explore available DNA or protein sequence databases. BLAST may generate a huge output for a large sequence data that contains various sequence patterns. However, BLAST does not provide a tool to summarize and analyze the patterns or matched alignments in the BLAST output file. BLAST lacks of general and robust parsing tools to extract the essential information out from its output. This paper presents a pattern summary system which is a powerful and comprehensive tool for discovering pattern structures in huge amount of sequence data in the BLAST. The pattern summary system can identify clusters of patterns, extract the cluster pattern sequences from the subject database of BLAST, and display the clusters graphically to show the distribution of clusters in the subject database.

• The Journal of Korean Institute of Communications and Information Sciences
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• v.29 no.3A
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• pp.248-256
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• 2004

Woerner had suggested an asynchronous trellis-coded DS/CDMA system based on a multi-sequence signaling, biorthogonal sequence, which is superior to single sequence signaling, such as M-ary PSK, due to their better cross-correlation properties. This paper analyzes and compares system performance between OPSM, a recently-presented multi-sequence signaling scheme, and biorthogonal sequence signaling. Interuser interference moments of the two schemes are derived and compared which verifies that OPSM, having smaller signature sequences per symbol than biorthogonal signaling, reduces cross-correlation. Numerical results compare the power and spectral efficiency of asynchronous trellis-coded DS/CDMA systems based on multi-sequence signaling.

• Kyungpook Mathematical Journal
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• v.62 no.1
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• pp.107-118
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• 2022

In this note we observe that any truncated multi-index sequence has an interpolating measure supported in Euclidean space. It is well known that the consistency of a truncated moment sequence is equivalent to the existence of an interpolating measure for the sequence. When the moment matrix of a moment sequence is nonsingular, the sequence is naturally consistent; a proper perturbation to a given moment matrix enables us to confirm the existence of an interpolating measure for the moment sequence. We also illustrate how to find an explicit form of an interpolating measure for some cases.

• Korean Journal of Computational Design and Engineering
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• v.18 no.6
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• pp.417-427
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• 2013

Assembly direction is used in order to confirm the generated assembly sequences in an automatic assembly sequence planning system. Moreover, assembly sequence planners can ascertain the feasibility of a sequence during simulation with assembly direction based in a CAD environment. In other words, assembly direction is essential for sequence optimizing and automatic generation. Based on the importance of assembly direction, this paper proposes a method to select the best direction for the generated assembly sequence using disassembly simulation and geometrical common area between assembled parts. Simultaneously, this idea can be applied to verify the generated assembly sequence. In this paper, the automatic selection of assembly direction and sequence correction system is designed and implemented. The developed algorithms and the implemented system are verified based on case study in the CAD environment.

• Animal cells and systems
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• v.3 no.1
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• pp.69-72
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• 1999

A tandemly repeated DNA sequence was identified and characterized y the combined RAPD and FISH data from a total genomic DNA of Welsh onion (Allium fistulosum). A clone containing this repeating sequence was selected and sequenced. This repeating unit of 314 bp inserted into pAf 072 contained 54.1% adenine and thymine residues, and showed the primer sequence used, 5'-GAAACGGGTG-3', in both terminals of the sequence. Fluorescence in situ hybridization using this tandemly repeated sequence as a probe indicated that the detected sites were coincident with the major C-banded constitutive heterochromatin in the terminal regions of both arms of all 6 chromosomes.