• Bioinformatics and Biosystems
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• v.1 no.2
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• pp.89-94
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• 2006

Mass spectrometry (MS) is widely applied for high throughput proteomics analysis. When large-scale proteome analysis experiments are performed, it generates massive amount of data. To search these proteomics data against protein databases, fully automated database search algorithms, such as Mascot and SEQUEST are routinely employed. At present, it is critical to reduce false positives and false negatives during such analysis. In this review we have focused on aspects of automated protein identification using tandem mass spectrometry (MS/MS) spectra and validation of the protein identifications of two most common automated protein identification algorithms Mascot and SEQUEST.

• Korean Journal of Microbiology
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• v.30 no.4
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• pp.278-285
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• 1992

Chemotaxonomic and numerical identification were carried out for a isolate of Streptomyces strain SMF301 producing spores in submerged culture. Fifty taxonomic unit characters were tested and the data were analyzed numerically using the TAXON program. The isolate SMF301 was identified to cluster 1A of Streptomyces and best matched to Streptomyces limosus which is a synonym of Streptomyces albidoflavus. Therefore, it was concluded that the isolate was identified to be a member of Streptomyces alidoflavus.

• Parasites, Hosts and Diseases
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• v.54 no.6
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• pp.743-750
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• 2016

Mus musculus (Rodentia: Muridae) has generally been infected with a rodent hookworm Nippostrongylus brasiliensis. In this report, we present morphological and molecular identification of N. brasiliensis by light and scanning electron microscopy and PCR amplification of mitochondrial cytochrome c oxidase subunit 1 (cox1) gene and the protein sequences encoded by cox1 gene, respectively. Despite the use of N. brasiliensis in many biochemistry studies from India, their taxonomic identification was not fully understood, especially at the species level, and no molecular data is available in GenBank from India. Sequence analysis of cox1 gene in this study revealed that the present specimen showed close identity with the same species available in GenBank, confirming that the species is N. brasiliensis. This study represents the first record of molecular identification of N. brasiliensis from India and the protein structure to better understand the comparative phylogenetic characteristics.

• Korean Journal of Microbiology
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• v.30 no.5
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• pp.415-420
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• 1992

Numerical identification was carried out for an isolate of Streptomyces strain producing the extracellular .betha.-lactamase inhibitor. Fifty taxonbomic unit characters were tested and the data were analyzed numerically using the TAXON program. The isoalte was identified to the majro cluster 5 of Streptomyces and it was best matched to Strepstomyces omiyaensis which is a synonym of Streptomyces exfoliatus. Therefore, it was concluded that the isolate was identified to be a strain (SMF19) of Streptomyces exfoliatus.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.50 no.4
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• pp.447-452
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• 2017

In this study, we tried to identify a sea anemone collected from the coast of Gijang, Busan. The anemone was morphologically similar to species belonging to the genus Anthopleura, but its morphological characteristics did not allow for confirmed identification to species level. Multiple genes from mitochondrial cytochrome oxidase III, 12S and 16S rRNA, and nuclear 18S and 28S rRNA, were amplified for multilocus sequence typing (MLST) analysis using genomic DNA extracted from the sampled anemone and a different primer set. Based on the MLST analysis, the anemone obtained in this study was identified as Anthopleura artemisia. Also, the sequence of internal transcribed spacer-2 was most closely related to A. artemisia, indicating that this single region might be useful for anemone identification. This study shows significance of molecular identification for sea anemones, and will be helpful in studies of sea anemone identification using genotyping-by-sequencing.

• Horticultural Science & Technology
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• v.30 no.5
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• pp.549-556
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• 2012

The study aimed to establish an efficient tool for cultivar identification and characterization being the first steps of apple introduction and improvement program. We utilized a method to efficiently record DNA molecular fingerprints of plant individuals genotyped by RAPD, which could be used as efficient reference information for quick plant identification. Ten of sixty 11-mer primers were screened to identify the 68 apple genotypes which could be distinguished by a combination of several primers. All cultivars were easily identified by the corresponding primers marked on the cultivar identification diagram (CID). The results indicated that the CID strategy developed and employed in the apple cultivar identification could be vital in the utilization of DNA marker in other plants as well as the development of the apple industry.

• Korean Journal of Environmental Biology
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• v.41 no.2
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• pp.145-166
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• 2023

Parrots have been threatened by global trade to meet their high demand as pets. Controlling parrot trade is essential because parrots play a vital role in the ecosystem. Accurate species identification is crucial for controlling parrot trade. Parrots have been traded as eggs due to their advantages of lower mortality rates and more accessible transport than live parrots. A molecular method is required to identify parrot eggs because it is difficult to perform identification using morphological features. In this study, DNAs were obtained from 43 unidentified parrot eggs using a non-destructive sampling method. Partial cytochrome b (CYTB) gene was then successfully amplified using polymerase chain reaction (PCR) and sequenced. Sequences newly obtained in the present study were compared to those available in the GenBank by database searching. In addition, phylogenetic analysis was conducted to identify species using available sequences in GenBank along with sequences reported in previous studies. Finally, the 43 parrot eggs were successfully identified as seven species belonging to two families and seven genera. This non-destructive sampling method for obtaining DNA and molecular identification might help control the trade of parrot eggs and prevent their illegal trade.

• Animal Systematics, Evolution and Diversity
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• v.28 no.1
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• pp.36-41
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• 2012

The larvae of Chaoborus are widely distributed in lakes, ponds, and reservoirs. These omnivorous Chaoborus larvae are crucial predators and play a role in structuring zooplankton communities, especially for small-sized prey. Larvae of Chaoborus are commonly known to produce predator-induced polyphenism in Daphnia sp. Nevertheless, their taxonomy and molecular phylogeny are very poorly understood. As a fundamental study for understanding the role of Chaoborus in predator-prey interactions in a freshwater ecosystem, the molecular identification and phylogenetic relationship of Chaoborus were analyzed in this study. A molecular comparison based on partial mitochondrial cytochrome oxidase I (COI) between species in Chaoborus was carried out for the identification of Chaoborus larvae collected from 2 localities in Korea. According to the results, the Chaoborus species examined here was identified as C. flavicans, which is a lake-dwelling species. Furthermore, partial mitochondrial genome including COI, COII, ATP6, ATP8, COIII, and ND3 were also newly sequenced from the species and concatenated 5 gene sequences excluding ATP8 with another 9 dipteran species were compared to examine phylogenetic relationships of C. flavicans. The results suggested that Chaoborus was more related to the Ceratopogonidae than to the Culicidae. Further analysis based on complete mitochondrial DNA sequences and nuclear gene sequences will provide a more robust validation of the phylogenetic relationships of Chaoborus within dipteran lineages.

• Journal of Microbiology
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• v.33 no.2
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• pp.95-102
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• 1995

A probability identification matrix of acidophilic Streptomyces was constructed. The phenetic data of the strains were derived from numerical classification described by Seong et al. The minimum number of diagnostic characters was determined using computer programs for calculation of different separation indices. The resulting matrix consisted of 25 clusters versus 53 characters. Theoretical evaluation of this matrix was achieved by estimating the chuster overlap and the identification scores for the Hypothetical Median Organisms (HMO) and for the representatives of each cluster. Cluster overlap was found to be relatively small. Identification scores for the HMO and the randomly selected representatives of each cluster were satisfactory. The matrix was assessed practically by applying the matrix to the identification of unknown isolates. Of the unknown isolates, 71.9% were clearly identified to one of eight clusters. The numerical classification data was also used to design a selective isolation medium for antibiotic-producing organisms. Four chemical substances including 2 antibiotics were determined by the DLACHAR program as diagnostic for the isolation of target organisms which have antimicrobial activity against Micrococcus luteus. It was possible to detect the increased rate of selective isolation on the synthesized medium. Theresults show that the numerical phenetic data can be applied to a variety of purposes, such as construction of identification matrix and selective isolation medium for acidophilic antinomycetes.

• BMB Reports
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• v.37 no.1
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• pp.11-27
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• 2004

The introduction of molecular markers in genetic analysis has revolutionized medicine. These molecular markers are genetic variations associated with a predisposition to common diseases and individual variations in drug responses. Identification and genotyping a vast number of genetic polymorphisms in large populations are increasingly important for disease gene identification, pharmacogenetics and population-based studies. Among variations being analyzed, single nucleotide polymorphisms seem to be most useful in large-scale genetic analysis. This review discusses approaches for genetic analysis, use of different markers, and emerging technologies for large-scale genetic analysis where millions of genotyping need to be performed.