• The Journal of the Convergence on Culture Technology
• /
• v.5 no.3
• /
• pp.339-344
• /
• 2019

Global sequence alignment in search of similarity or homology favors larger size of the sequence because it keeps looking for more similar section between two sequences in the hope that it adds up scores for matched part in the rest of the sequence. If a substantial size of mismatched section exists in the middle of the sequence, it greatly reduces the total alignment score. In this case a whole sequence would be better to be divided into multiple sections. Overall alignment score over the multiple sections of the sequence would increase as compared to global alignment. This method is called multiple local alignment. In this paper, we implement a multiple local alignment algorithm, an extension of Smith-Waterman algorithm and show the experimental results for the algorithm that is able to search for sub-optimal sequence.

• Proceedings of the Korean Institute of Intelligent Systems Conference
• /
• 2003.09a
• /
• pp.264-267
• /
• 2003

Multiple sequence alignment is a useful tool to identify the relationships among protein sequences. Dynamic programming is the most widely used algorithm to obtain multiple sequence alignment with optimal cost. However dynamic programming cannot be applied to certain cost function due its drawback and to produce optimal multiple sequence alignment. We proposed sub-alignment refinement algorithm to overcome the problem of dynamic programming and impelmented this algorithm as a module of our MS Windows-based sequence alignment program.

• Journal of KIISE:Software and Applications
• /
• v.30 no.9
• /
• pp.803-811
• /
• 2003

Multiple sequence alignment is a useful tool to identify the relationships among protein sequences. Dynamic programming is the most widely used algorithm to obtain multiple sequence alignment with optimal cost. However, dynamic programming cannot be applied to certain cost function due to its drawback and cannot be used to produce optimal multiple sequence alignment. We propose sub-alignment refinement algorithm to overcome the problem of dynamic programming. Also we show proposed algorithm can solve the problem of dynamic programming efficiently.

• Korean Journal of Microbiology
• /
• v.35 no.2
• /
• pp.115-120
• /
• 1999

Multiple Sequence Alignment of DNA and protem sequences is a imnport'mt tool in the study of molecular evolution, gene regulation. and prolein suucture-function relationships. Progressive pairwise alignment method generates multiple sequence alignment fast but not necessarily with optimal costs. Dynamic programming generates multiple sequence alig~~menl with optimal costs in most cases but long execution time. In this paper. we suggest genetlc algorithm lo improve the multiple sequence alignment generated from the cnlent methods, describe the design of the genetic algorithm, and compare the multiple sequence alignments from 0111 method and current methods.

• Journal of KIISE:Computer Systems and Theory
• /
• v.32 no.11_12
• /
• pp.578-586
• /
• 2005

In this Paper we consider the problem of sequence alignment with quality scores. DNA sequences produced by a base-calling program (as part of sequencing) have quality scores which represent the confidence level for individual bases. However, previous sequence alignment algorithms do not consider such quality scores. To solve sequence alignment with quality scores, we propose a measure of an alignment of two sequences with orality scores. We show that an optimal alignment in this measure can be found by dynamic programming.

• 제어로봇시스템학회:학술대회논문집
• /
• 2003.10a
• /
• pp.273-277
• /
• 2003

A general process of electronic assembly is composed of a series of geometric alignments and bonding/screwing processes. After assembly, the function is tested in a following process of inspection. However, assembly of micro-optic devices requires both processes to be performed in equipment. Coarse geometric alignment is made by using vision and optical function is improved by the following fine motion based on feedback of tunable laser interferometer. The general system is composed of a precision robot system for 3D assembly, a 3D vision guided system for geometric alignment and an optical feedback system with a tunable laser. In this study, we propose a new fast alignment algorithm of micro-optic devices for both of visual and optical alignments. The main goal is to find a fastest alignment process and algorithms with state-of-the-art technology. We propose a new approach with an optimal sequence of processes, a visual alignment algorithm and a search algorithm for an optimal optical alignment. A system is designed to show the effectiveness and efficiency of the proposed method.

• Journal of KIISE:Software and Applications
• /
• v.34 no.5
• /
• pp.397-406
• /
• 2007

The problem of finding an optimal alignment between sequence A and B can be solved by dynamic programming algorithm(DPA) efficiently. But, if the length of string was longer, the problem might not be solvable because it requires O(m*n) time and space complexity.(where, $m={\mid}A{\mid},\;n={\mid}B{\mid}$) For space, Hirschberg developed a linear space and quadratic time algorithm, so computer memory was no longer a limiting factor for long sequences. As computers's processor and memory become faster and larger, a method is needed to speed processing up, although which uses more space. For this purpose, we present an algorithm which will solve the problem in quadratic time and linear space. By using division method, It computes optimal alignment faster than LSA, although requires more memory. We generalized the algorithm about division problem for not being divided into integer and pruned additional space by entry/exit node concept. Through the proofness and experiment, we identified that our algorithm uses d*(m+n) space and a little more (m*n) time faster than LSA.

• The Journal of the Korea Contents Association
• /
• v.16 no.10
• /
• pp.608-616
• /
• 2016

The Smith-Watrman (SW) algorithm is a local alignment algorithm which is one of important operations in DNA sequence analysis. The SW algorithm finds the optimal local alignment with respect to the scoring system being used, but it has a problem to demand long execution time. To solve the problem of SW, some methods to perform SW in distributed and parallel manner have been proposed. The ADAM which is a distributed and parallel processing framework for DNA sequence has parallel SW. However, the parallel SW of the ADAM does not consider that the SW is a dynamic programming method, so the parallel SW of the ADAM has the limit of its performance. In this paper, we propose a method to enhance the parallel SW of ADAM. The proposed parallel SW (PSW) is performed in two phases. In the first phase, the PSW splits a DNA sequence into the number of partitions and assigns them to multiple nodes. Then, the original Smith-Waterman algorithm is performed in parallel at each node. In the second phase, the PSW estimates the portion of data sequence that should be recalculated, and the recalculation is performed on the portions in parallel at each node. In the experiment, we compare the proposed PSW to the parallel SW of the ADAM to show the superiority of the PSW.

• Journal of Microbiology and Biotechnology
• /
• v.14 no.5
• /
• pp.1022-1030
• /
• 2004

The gene encoding Aquifex pyrophilus (Apy) DNA polymerase was cloned and sequenced. The Apy DNA polymerase gene consists of 1,725 bp coding for a protein with 574 amino acid residues. The deduced amino acid sequence of Apy DNA. polymerase showed a high sequence homology to Escherichia coli DNA polymerase I-like DNA polymerases. It was deduced by amino acid sequence alignment that Apy DNA polymerase, like the Klenow fragment, has only the two domains, the $3'{\rightarrow}5'$ exonuclease domain and the $5'{\rightarrow}3'$ polymerase domain, containing the characteristic motifs. The Apy DNA polymerase gene was expressed under the control of T7lac promoter on the expression vector pET-22b(+) in E. coli. The expressed enzyme was purified by heat treatment, and Cibacron blue 3GA and $UNO^{TM}$ Q column chromatographies. The optimum pH of the purified enzyme was 7.5, and the optimal concentrations of KCl and $Mg^{2+}$ were 20 mM and 3 mM, respectively. Apy DNA polymerase contained a double strand-dependent $3'{\rightarrow}5'$ proofreading exonuclease activity, but lacked any detectable $5'{\rightarrow}3'$ exonuclease activity, which is consistent with its amino acid sequence. The somewhat lower thermostability of Apy DNA polymerase than the growth temperature of A. pyrophilus was analyzed by the comparison of amino acid composition and pressure effect.

• Journal of Environmental Science International
• /
• v.11 no.1
• /
• pp.33-40
• /
• 2002

An antimicrobial substance-producing microorganism was isolated from soil samples. Based of the taxonomic characteristics of its morphological, cultural, physiological properties and 16s rRNA sequence alignment, this microorganism was identified as Pseudomonas aeruginosa, and we named Pseudomonas aeruginosa EL-KM. The optimal culture condition for production of antimicrobial substance was 1% mannitol, 0.4% yeast extract, 0.5% Nacl, 0.2% $K_2SO_4$, 100$\mu$M $MgSO_4$.$7H_2O$, 10$\mu$M $CaCl_2$.$2H_2O$, 1$\mu$M $FeSO_4$.$7H_2O$, 1$\mu$M $MnSO_4$.$4-5H_2O$, initial pH 7 and 200 rpm at 3$0^{\circ}C$. The purification of the antimicrbial substance was performed by silica gel column chromatographys, and fraction with TLC $R_f$ 0.77 value represented good antimicrobial activity. The crude antimicrbial substance was stable within a pH range of 3-10 and temperature range of 4$^{\circ}C$-121$^{\circ}C$ autoclaving. This crude antibacterial substance acted as bacteriolytic agent against Vibrio cholerae non-Ol ATCC 25872, and also exhibited excellent properties, when the substance was demonstrated against many other gram-positive, gram-negative bacteria, yeast and fungi.