• The KIPS Transactions:PartB
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• v.14B no.6
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• pp.461-472
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• 2007

The emphasis in genome projects has Been moving towards the sequence analysis in order to extract biological "meaning"(e.g., evolutionary history of particular molecules or their functions) from the sequence. Especially. palindromic or direct repeats that appear in a sequence have a biophysical meaning and the problem is to recognize interesting patterns and configurations of words(strings of characters) over complementary alphabets. In this paper, we propose an algorithm to identify variable length palindromic pairs(longer than a threshold), where we can allow gaps(distance between words). The algorithm is called palindrome algorithm(PA) and has O(N) time complexity. A palindromic pair consists of a hairpin structure. By composing collected palindromic pairs we build n-pair palindromic patterns. In addition, we dot some of the longest pairs in a circle to represent the structure of a DNA sequence. We run the algorithm over several selected genomes and the results of E.coli K12 are presented. There existed very long palindromic pair patterns in the genomes, which hardly occur in a random sequence.

• The Journal of Korean Institute of Communications and Information Sciences
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• v.28 no.10C
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• pp.995-1006
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• 2003

It is well know that in the wireless communication systems the transmitted signals can suffer from multipath fading due to the wave propagation characteristics and the obstacles over the paths, resulting in serious reduction in the power of the received signals. However, it is possible to take advantage of the inherent diversity imposed in the multipath reception if the underlying channel can be properly estimated. One of the diversity reception methods in this case is Rake processing. In this paper we study the Rake receivers for the direct-sequence spread-spectrum communication systems utilizing PN (pseudo noise) sequences to achieve spread spectrum. A conventional Rake receiver can use the finite-duration impulse (FIR) filter followed by the PN sequence demodulator, where the FIR filter coefficients are the reverse-ordered complex conjugate values of the fading channel impulse response estimates. Here, we propose a new Rake processing method by replacing the aforementioned PN code sequence with a new set of optimum demodulator coefficients. More specifically, the concept of the new optimum Rake processing is first introduced and then the optimum demodulator coefficients are theoretically derived. The performance obtained using the new optimum Rake processing is also calculated. The analytical results are verified by computer simulation. As a result, it is shown that the new optimum Rake processing method improves the MSE performance more than 10 dB over the conventional one using the fixed PN sequence demodulator. It is also shown that the new optimum Rake processing method improves the MSE performance about 10 dB over the Adaptive Correlator that performs the combining of the multipath components and PN demodulation concurrently. And finally, the MSE performance of the optimum Rake demodulator is very close to the MSE performance of OPSK demodulator under the AWGN channel.

• International Journal of Industrial Entomology and Biomaterials
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• v.1 no.2
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• pp.165-169
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• 2000

We have constructed cDNA library from the larvae whole body of the firefly, Pyrocoelia rufa. Single direct partial sequencing of anonymous cDNA clones was performed to obtain genetic information on the firefly, P. rufa, of which genetic information is currently not available. This expressed sequence tags (EST) analysis of the 54 clones (54%) showed significant homology to the known genes registered in GenBank. Of these clones, twenty-four were related to the known insect genes, but these clones were not matched to previously identified firefly genes. Putative functional categories of these clones showed that the next abundant genes were associated with energy metabolism.

• Journal of Communications and Networks
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• v.1 no.3
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• pp.182-188
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• 1999

The optimal joint maximum-likelihood sequence estima-for using an array of antennas is derived for synchronous direct sequence-code division multiple access (DS-CDMA) system. Each user employs a rate 1/n convolutional code for channel coding for the additive white Gaussian noise (AWGN) channel. The array re-ceiver structure is composed of beamformers in the users' direc-tions followed by a bank of matched filters. The decoder is imple-mented using a Viterbi algorithm whose states depend on the num-ber of users and the constraint length of the convolutional code. The asymptotic array multiuser coding gain(AAMCG)is defined to encompass the asymptotic multiuser coding gain and the spatial information on users' locations in the system. We derive the upper and lower bounds of the AAMCG. As an example, the upper and lower bounds of AAMCG are obtained for the two user case where each user employes the maximum free distance convolutional code with rate 1/2. The enar-far resistance property is also investigated considering the number of antenna elements and user separations in the space.

• Environmental Engineering Research
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• v.12 no.5
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• pp.231-237
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• 2007

The microbial eco-physiology has been the vital key of microbial ecological research. Unfortunately, available methods for direct identity of microorganisms and for the investigation of their activity in complicated community dynamics are limited. In this study, metagenomics was considered as a promising functional genomics tool for improving our understanding of microbial eco-physiology. Its potential applications and challenges were also reviewed. Because of tremendous diversity in microbial populations in environment, sequence analysis for whole metagenomic libraries from environmental samples seems to be unrealistic to most of environmental engineering researchers. When a target function is of interest, however, sequence analysis for whole metagenomic libraries would not be necessary. For this case, nucleic acids of active populations of interest can be selectively gained using another cutting-edge functional genomic tool, SIP (stable isotope probing) technique. If functional genomes isolated by SIP can be transferred into metagenomic library, sequence analysis for such selected functional genomes would be feasible because the reduced size of clone library may become adequate for sequencing analysis. Herein, integration of metagenomics with SIP was suggested as a novel functional genomics approach to study microbial eco-physiology in environment.

• Biotechnology and Bioprocess Engineering:BBE
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• v.6 no.4
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• pp.306-308
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• 2001

A recombinant human growth hormone(hGH) was expressed as a secretory product in the yeast Saccharomyuces cerevisiae. There different leader sequences derived from the mating fac-tor $\alpha$1(MF$\alpha$1) inulinase and invertase were used to direct the secretion of hGH into the extracel-lular medium. Among three leader sequences tested, the inulinase leader sequence was found to be the most efficient in the secretory expression of hGH. In contrast, no hGH was detected in the ex-tracellular medium with the invertase leader sequence. After 48 h shake-flask culture, the yields of hGH secreted into th emedium by the invertase. MF$\alpha$1 inulinase and invertase leader sequences were approximately 0, 0.3 and 0.9 mg/L, respectively. The secretion efficiencies were also found to be 0, 3.8 and 13% for the invertase , MG$\alpha$1 and inulinase leader sequences, respectively.

• Proceedings of the Materials Research Society of Korea Conference
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• 2011.05a
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• pp.10.2-10.2
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• 2011

The design and synthesis of protein-like polymers is a fundamental challenge in materials science. A biomimetic approach is to explore the impact of monomer sequence on non-natural polymer structure and function. We present the aqueous self-assembly of two peptoid polymers into extremely thin two-dimensional (2D) crystalline sheets directed by periodic amphiphilicity, electrostatic recognition and aromatic interactions. Peptoids are sequence-specific, oligo-N-substituted glycine polymers designed to mimic the structure and functionality of proteins. Mixing a 1:1 ratio of two oppositely charged peptoid 36 mers of a specific sequence in aqueous solution results in the formation of giant, free-floating sheets with only 2.7 nm thickness. Direct visualization of aligned individual peptoid chains in the sheet structure was achieved using aberration-corrected transmission electron microscopy. Specific binding of a protein to ligand-functionalized sheets was also demonstrated. The synthetic flexibility and biocompatibility of peptoids provide a flexible and robust platform for integrating functionality into defined 2D nanostructures. In the later part of my talk, we describe the use of metal ions to construct two-dimensional hybrid films that have the ability to self-heal. Incubation of biomimetic peptoid polymers with specific divalent metal ions results in the spontaneous formation of uniform multilayers at the air-water interface. We anticipate that ease of synthesis and transfer of these two-dimensional materials may have many potential applications in catalysis, gas storage and sensing, optics, nanomaterial synthesis, and environmentally responsive scaffolds.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2000.11a
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• pp.17-20
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• 2000

Structural genomics aims to provide a good experimental structure or computational model of every tractable protein in a complete genome. Underlying this goal is the immense value of protein structure, especially in permitting recognition of distant evolutionary relationships for proteins whose sequence analysis has failed to find any significant homolog. A considerable fraction of the genes in all sequenced genomes have no known function, and structure determination provides a direct means of revealing homology that may be used to infer their putative molecular function. The solved structures will be similarly useful for elucidating the biochemical or biophysical role of proteins that have been previously ascribed only phenotypic functions. More generally, knowledge of an increasingly complete repertoire of protein structures will aid structure prediction methods, improve understanding of protein structure, and ultimately lend insight into molecular interactions and pathways. We use computational methods to select families whose structures cannot be predicted and which are likely to be amenable to experimental characterization. Methods to be employed included modern sequence analysis and clustering algorithms. A critical component is consultation of the presage database for structural genomics, which records the community's experimental work underway and computational predictions. The protein families are ranked according to several criteria including taxonomic diversity and known functional information. Individual proteins, often homologs from hyperthermophiles, are selected from these families as targets for structure determination. The solved structures are examined for structural similarity to other proteins of known structure. Homologous proteins in sequence databases are computationally modeled, to provide a resource of protein structure models complementing the experimentally solved protein structures.

• BMB Reports
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• v.42 no.5
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• pp.271-276
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• 2009

Sweetpotato (Ipomoea batatas (L). Lam.) is relatively tolerant to unfavorable growth conditions such as drought, yet has not been exploited to provide a better understanding of the molecular basis of drought stress tolerance. We obtained 983 high-quality expressed sequence tags of 100 bp or longer (average length of 700 bp) from cDNA libraries of detached white fibrous root tissues by subjecting them to dehydration for 6 h. The 431 cDNAs were each assigned a function by alignment using the BLASTX algorithm. Among them, three genes associated with various abiotic stresses and nine genes not previously associated with drought stress were selected for expression pattern analysis through detailed reverse transcription-polymerase chain reaction. The direct and indirect relationships of the 12 genes with drought tolerance mechanisms were ascertained at different developmental stages and under various stress conditions.

• Journal of the Institute of Electronics Engineers of Korea TC
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• v.47 no.6
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• pp.42-48
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• 2010

Joint Tactical Information Distribution System (JTIDS) uses cyclic code shift keying (CCSK) for baseband symbol modulation, in which 5-bit information is mapped to one of thirty two 32-chip sequences. It is a kind of direct sequence based spread spectrum communication. In this paper, the performance of non-coherent detection of CCSK using non-orthogonal 32-chip sequence is evaluated. And a 32-chip sequence with better performance is also proposed and compared with the conventional one.