• The KIPS Transactions:PartD
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• v.12D no.1 s.97
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• pp.43-50
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• 2005

The Processing domains of spatio-temporal databases are divided into time-series databases for moving objects and sequence databases for discrete historical objects. Recently the selectivity estimation techniques for query optimization in spatio-temporal databases have been studied, but focused on query optimization in time-series databases. There wat no previous work on the selectivity estimation techniques for sequence databates as well. Therefore, we construct T-Minskew histogram for query optimization In sequence databases and propose a selectivity estimation method using the T-Minskew histogram. Furthermore we propose an effective histogram maintenance technique for food performance of the histogram.

• 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.

• Journal of KIISE:Databases
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• v.30 no.4
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• pp.372-380
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• 2003

Temporal databases support time-varying events so that conventional aggregate functions are extended to be processed with time for temporal aggregate functions. In the previous approach, it is done repeatedly to find time intervals and is calculated the result of each interval whenever target events are different. This paper proposes a method which processes temporal aggregate function queries using time point sequence. We can make time point sequence storing the start time and the end time of events in temporal databases in advance. It is also needed to update time point sequence due to insertion or deletion of events in temporal databases. Because time point sequence maintains the information of time intervals, it is more efficient than the previous approach when temporal aggregate function queries are continuously requested, which have different target events.

• Journal of KIISE:Databases
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• v.34 no.1
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• pp.84-97
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• 2007

Selectivity estimation techniques in query optimization have been used in commercial databases and histograms are popularly used for the selectivity estimation. Recently, the techniques for spatio-temporal databases have been restricted to existing temporal and spatial databases. In addition, the selectivity estimation techniques focused on time-series data such as moving objects. It is also impossible to estimate selectivity for range queries with a time interval. Therefore, we construct two histograms, CMH (current multidimensional histogram) and PMH (past multidimensional histogram), to estimate the selectivity of multidimensional sequence data in spatio-temporal databases and propose effective selectivity estimation methods using the histograms. Furthermore, we solve a problem about the range query using our proposed histograms. We evaluated the effectiveness of histograms for range queries with a time interval through various experimental results.

• The Journal of the Korea Contents Association
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• v.11 no.12
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• pp.52-59
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• 2011

In this paper, we propose an indexing method to support efficient similarity search for sequence databases. We present a new distance measurement called minimum DTW distance to enhance the filtering effects. The minimum DTW distance is to measure the minimum distance between a sequence data and the group of similar sequences. It enables similarity search through hierarchical index structure by filtering sequence databases. Finally, we show the superiority of our method through some experiments.

• Journal of KIISE:Databases
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• v.32 no.1
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• pp.24-42
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• 2005

Characteristics of biological data including genome sequences are heterogeneous and various. Although the need of management systems for genome sequencing which should reflect biological characteristics has been raised, most current biological databases provide restricted function as repositories for biological data. Therefore, this paper describes a management system of nucleotide sequences at the level of biological laboratories. It includes format transformation, editing, storing and retrieval for collected nucleotide sequences from public databases, and handles sequence produced by experiments. It uses BSML based on XML as a common format in order to extract data fields and transfer heterogeneous sequence formats. To manage sequences and their changes, version management system for originated DNA is required so as to detect transformed new sequencing appearance and trigger database update. Our experimental results show that applying active trigger rules to manage changes of sequences can automatically store changes of sequences into databases.

• Journal of Korea Multimedia Society
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• v.7 no.11
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• pp.1505-1514
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• 2004

Sequence matching in time-series databases is an operation that finds the data sequences whose changing patterns are similar to that of a query sequence. Typically, sequence matching hires a multi-dimensional index for its efficient processing. In order to alleviate the dimensionality curse problem of the multi-dimensional index in high-dimensional cases, the previous methods for sequence matching apply the Discrete Fourier Transform(DFT) to data sequences, and take only the first two or three DFT coefficients as organizing attributes of the multi-dimensional index. This paper first points out the problems in such simple methods taking the firs two or three coefficients, and proposes a novel solution to construct the optimal multi -dimensional index. The proposed method analyzes the characteristics of a target database, and identifies the organizing attributes having the best discrimination power based on the analysis. It also determines the optimal number of organizing attributes for efficient sequence matching by using a cost model. To show the effectiveness of the proposed method, we perform a series of experiments. The results show that the Proposed method outperforms the previous ones significantly.

• Plant Biotechnology Reports
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• v.2 no.1
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• pp.59-73
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• 2008

Several aspects of photoperception and light signal transduction have been elucidated by studies with model plants. However, the information available for economically important crops, such as Fabaceae species, is scarce. In order to incorporate the existing genomic tools into a strategy to advance soybean research, we have investigated publicly available expressed sequence tag (EST) sequence databases in order to identify Glycine max sequences related to genes involved in light-regulated developmental control in model plants. Approximately 38,000 sequences from open-access databases were investigated, and all bona fide and putative photoreceptor gene families were found in soybean sequence databases. We have identified G. max orthologs for several families of transcriptional regulators and cytoplasmic proteins mediating photoreceptor-induced responses, although some important Arabidopsis phytochrome-signaling components are absent. Moreover, soybean and Arabidopsis genefamily homologs appear to have undergone a distinct expansion process in some cases. We propose a working model of light perception, signal transduction and response-eliciting in G. max, based on the identified key components from Arabidopsis. These results demonstrate the power of comparative genomics between model systems and crop species to elucidate several aspects of plant physiology and metabolism.

• Journal of Industrial Technology
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• v.20 no.B
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• pp.219-226
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• 2000

In this paper, we propose a new novel method for similarity search that supports time warping. Our primary goal is to innovate on search performance in large databases without false dismissal. To attain this goal, we devise a new distance function $D_{tw-lb}$ that consistently underestimates the time warping distance and also satisfies the triangular inequality. $D_{tw-lb}$ uses a 4-tuple feature vector extracted from each sequence and is invariant to time warping. For efficient processing, we employ a multidimensional index that uses the 4-tuple feature vector as indexing attributes and $D_{tw-lb}$ as a distance function. We prove that our method does not incur false dismissal. To verify the superiority of our method, we perform extensive experiments. The results reveal that our method achieves significant speedup up to 43 times with real-world S&P 500 stock data.

• Journal of KIISE:Databases
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• v.31 no.6
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• pp.650-663
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• 2004

In molecular biology, DNA sequence searching is one of the most crucial operations. Since DNA databases contain a huge volume of sequences, a fast indexing mechanism is essential for efficient processing of DNA sequence searches. In this paper, we first identify the problems of the suffix tree in aspects of the storage overhead, search performance, and integration with DBMSs. Then, we propose a new index structure that solves those problems. The proposed index consists of two parts: the primary part represents the trie as bit strings without any pointers, and the secondary part helps fast accesses of the leaf nodes of the trio that need to be accessed for post processing. We also suggest an efficient algorithm based on that index for DNA sequence searching. To verify the superiority of the proposed approach, we conducted a performance evaluation via a series of experiments. The results revealed that the proposed approach, which requires smaller storage space, achieves 13 to 29 times performance improvement over the suffix tree.