• The Journal of the Korea Contents Association
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• v.10 no.7
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• pp.81-87
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• 2010

This paper proposes a G-BLAST(BLAST using Grid Computing) system, an integrated software package for BLAST searches operated in heterogeneous distributed environment. G-BLAST employed 'database splicing' method to improve the performance of BLAST searches using exists computing resources. G-BLAST is a basic local alignment search tool of DNA Sequence using grid computing in heterogeneous distributed environment. The G-BLAST improved the existing BLAST search performance in gene sequence analysis. Also G-BLAST implemented the pipeline and data management method for users to easily manage and analyze the BLAST search results. The proposed G-BLAST system has been confirmed the speed and efficiency of BLAST search performance in heterogeneous distributed computing.

• The Korea Journal of Herbology
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• v.21 no.2
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• pp.129-133
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• 2006

Objectives : Cervus elaphus species are some of the most medicinally important genera in the Oriental medicine. This study was performed to determine if Cenvus elaphus species could be identified by sequencing analysis and to verify Basic Local Alignment Search Tool (BLAST) search, which was used to assess genetic identification. Methods : The DNAs of Cervus elaphus species were extracted, amplified by PCR, and sequenced. The DNAs of Cervus species were identified by BLAST search in website. Results : By BLAST search one of Cervus elaphus species was identified as Cervus elaphussibericus but the other was identified as Cervus elaphus nelsoni. This work showed that identification can efficiently be performed by BLAST search. Conclusion : These results suggest that sequencing following BLAST search might be able to provide the identification of Cervus elaphus species.

• Bioinformatics and Biosystems
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• v.1 no.2
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• pp.99-102
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• 2006

The Basic Local Alignment Search Tool (BLAST) is one of the most established software in bioinformatics research and it compares a query sequence against the libraries of known sequences in order to investigate sequence similarity. Expressed Sequence Tags (ESTs) are single-pass sequence reads from mRNA (or cDNA) and represent the expression for a given cDNA library and the snapshot of genes expressed in a given tissue and/or at a given developmental stage. Therefore, ESTs can be very valuable information for functional genomics and bioinformatics researches. Although major bio database (DB) websites including NCBI are providing BLAST services and EST data, local DB and search system is demanding for better performance and security issue. Here we present animal EST DBs and local BLAST search system. The animal ESTs DB in NCBI Genbank were divided by animal species using the Perl script we developed. and we also built the new extended DB search systems fur the new data (Local Animal BLAST Search System: http://bioinfo.kohost.net), which was constructed on the high-capacity PC Cluster system fur the best performance. The new local DB contains 650,046 sequences for Bos taurus(cattle), 368,120 sequences for Sus scrofa (pig), 693,005 sequences for Gallus gallus (fowl), respectively.

• Journal of the Korea Society of Computer and Information
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• v.11 no.6 s.44
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• pp.69-78
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• 2006

In the field of the bioinformatics, it plays an important role in predicting functional information or structure information to search similar sequence in biological DB. Biolrgical sequences have been increased dramatically since Human Genome Project. At this point, because the searching speed for the similar sequence is highly regarded as the important factor for predicting function or structure, the SMP(Sysmmetric Multi-Processors) computer or cluster is being used in order to improve the performance of searching time. As the method to improve the searching time of BLAST(Basic Local Alighment Search Tool) being used for the similarity sequence search, We suggest the nBLAST algorithm performing on the cluster environment in this paper. As the nBLAST uses the MPI(Message Passing Interface), the parallel library without modifying the existing BLAST source code, to distribute the query to each node and make it performed in parallel, it is possible to easily make BLAST parallel without complicated procedures such as the configuration. In addition, with the experiment performing the nBLAST in the 28 nodes of LINUX cluster, the enhanced performance according to the increase in the number of the nodes has been confirmed.

• 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.

• Journal of Institute of Control, Robotics and Systems
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• v.12 no.10
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• pp.1044-1049
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• 2006

Multiple sequence alignment is a method to compare two or more DNA or protein sequences. Most of multiple sequence alignment tools rely on pairwise alignment and Smith-Waterman algorithm to generate an alignment hierarchy. Therefore, in the existing multiple alignment method as the number of sequences increases, the runtime increases exponentially. In order to remedy this problem, we adopted a parallel processing suffix tree algorithm that is able to search for common subsequences at one time without pairwise alignment. Also, the cross-matching subsequences triggering inexact-matching among the searched common subsequences might be produced. So, the cross-matching masking process was suggested in this paper. To identify the function of the clusters generated by suffix tree clustering, BLAST and CDD (Conserved Domain Database)search were combined with a clustering tool. Our clustering and annotating tool consists of constructing suffix tree, overlapping common subsequences, clustering gene sequences and annotating gene clusters by BLAST and CDD search. The system was successfully evaluated with 36 gene sequences in the pentose phosphate pathway, clustering 10 clusters, finding out representative common subsequences, and finally identifying functional domains by searching CDD database.

• Geomechanics and Engineering
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• v.35 no.2
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• pp.121-133
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• 2023

The demand for cement and limestone crushed materials has increased many folds due to the tremendous increase in construction activities in Pakistan during the past few decades. The number of cement production industries has increased correspondingly, and so the rock-blasting operations at the limestone quarry sites. However, the safety procedures warranted at these sites for the blast-induced ground vibrations (BIGV) have not been adequately developed and/or implemented. Proper prediction and monitoring of BIGV are necessary to ensure the safety of structures in the vicinity of these quarry sites. In this paper, an attempt has been made to predict BIGV using artificial neural network (ANN) at three selected limestone quarries of Pakistan. The ANN has been developed in Python using Keras with sequential model and dense layers. The hyper parameters and neurons in each of the activation layers has been optimized using randomized and grid search method. The input parameters for the model include distance, a maximum charge per delay (MCPD), depth of hole, burden, spacing, and number of blast holes, whereas, peak particle velocity (PPV) is taken as the only output parameter. A total of 110 blast vibrations datasets were recorded from three different limestone quarries. The dataset has been divided into 85% for neural network training, and 15% for testing of the network. A five-layer ANN is trained with Rectified Linear Unit (ReLU) activation function, Adam optimization algorithm with a learning rate of 0.001, and batch size of 32 with the topology of 6-32-32-256-1. The blast datasets were utilized to compare the performance of ANN, multivariate regression analysis (MVRA), and empirical predictors. The performance was evaluated using the coefficient of determination (R²), mean absolute error (MAE), mean squared error (MSE), mean absolute percentage error (MAPE), and root mean squared error (RMSE)for predicted and measured PPV. To determine the relative influence of each parameter on the PPV, sensitivity analyses were performed for all input parameters. The analyses reveal that ANN performs superior than MVRA and other empirical predictors, andthat83% PPV is affected by distance and MCPD while hole depth, number of blast holes, burden and spacing contribute for the remaining 17%. This research provides valuable insights into improving safety measures and ensuring the structural integrity of buildings near limestone quarry sites.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.407-411
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• 2005

KUGI (Korean UniGene Information) database contains the annotation information of the cDNA sequences obtained from the disease samples prevalent in Korean. A total of about 157,000 5'-EST high throughput sequences collected from cDNA libraries of stomach, liver, and some cancer tissues or established cell lines from Korean patients were clustered to about 35,000 contigs. From each cluster a representative clone having the longest high quality sequence or the start codon was selected. We stored the sequences of the representative clones and the clustered contigs in the KUGI database together with their information analyzed by running Blast against RefSeq, human mRNA, and UniGene databases from NCBI. We provide a web-based search engine fur the KUGI database using two types of user interfaces: attribute-based search and similarity search of the sequences. For attribute-based search, we use DBMS technology while we use BLAST that supports various similarity search options. The search system allows not only multiple queries, but also various query types. The results are as follows: 1) information of clones and libraries, 2) accession keys, location on genome, gene ontology, and pathways to public databases, 3) links to external programs, and 4) sequence information of contig and 5'-end of clones. We believe that the KUGI database and search system may provide very useful information that can be used in the study for elucidating the causes of the disease that are prevalent in Korean.

• Proceedings of the Korea Concrete Institute Conference
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• 1996.10a
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• pp.148-153
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• 1996

Concrete with ground granulated blast-furnace slag can be affected by frost attack because the reaction of hydration is slow at the early age. In this study, therefore, the freezing and thawing test has been carried out to investigate the freezing and thawing resistance on concrete with ground granulated blast-furnace slag. The freezing and thawing test has been performed on concrete a blended cement, which was substituted by ground granulated blast-furnace slag with 4 kinds of ratio (non-admixture, 20%, 40% and 60%). And also tested on concrete added the AE agents to the concrete of same mix proportion to search the improvement effects about the resistance. As a result, the freezing and thawing resistance showed a tendency of reduction in proportion to the increase of the substitution ratio. For non-AE concrete, resistances of the freezing and thawing were very poor as the durability index indicated less than 5.8%. For AE concrte, resistance of the freezing and thawing were excellent as the durability index indicated more than 80.9%.

• Structural Engineering and Mechanics
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• v.32 no.2
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• pp.269-282
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• 2009

Responding to the threat of terrorist attacks around the world, numerous studies have been conducted to search for new methods of vulnerability assessment and protective technologies for critical infrastructure under extreme bomb blasts or high velocity impacts. In this paper, a two-dimensional behavioral rate dependent lattice model (RDLM) capable of analyzing reinforced concrete members subjected to blast and impact loading is presented. The model inherently takes into account several major influencing factors: the progressive cracking of concrete in tension, the inelastic response in compression, the yielding of reinforcing steel, and strain rate sensitivity of both concrete and steel. A computer code using the explicit algorithm was developed based on the proposed lattice model. The explicit code along with the proposed numerical model was validated using experimental test results from the Woomera blast trial.