• Journal of KIISE:Databases
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• v.35 no.2
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• pp.125-131
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• 2008

It is very useful to predict orthologs for new genome annotation and research on genome evolution. We showed that the previous work can be extended to construct OCs(Ortholog Clusters) automatically from multiple complete-genomes. The proposed method also has the quality of production of InParanoid, which produces orthologs from just two genomes. On the other hand, in order to predict more exactly the function of a newly sequenced gene it can be an important issue to prevent unwanted inclusion of paralogs into the OCs. We have, here, investigated how well it is possible to construct a functionally purer OCs with score cut-offs. Our OCs were generated from the datasets of 20 procaryotes. The similarity with both COG(Clusters of Orthologous Group) and KO(Kegg Orthology) against our OCs has about 90% and inclines to increase with the growth of score cut-offs.

• Journal of Positioning, Navigation, and Timing
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• v.12 no.3
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• pp.257-269
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• 2023

This paper presents a method for detecting faults in data obtained from the Automatic Identification System (AIS) of surface vessels. The data include latitude, longitude, Speed Over Ground (SOG), and Course Over Ground (COG). We derive two methods that utilize two models: a constant state model and a derivative augmented model. The constant state model incorporates noise variables to account for state changes, while the derivative augmented model employs explicit variables such as first or second derivatives, to model dynamic changes in state. Generally, the derivative augmented model detects faults more promptly than the constant state model, although it is vulnerable to potentially overlooking faults. The effectiveness of this method is validated using AIS data collected at a harbor. The results demonstrate that the proposed approach can automatically detect faults in AIS data, thus offering partial assistance for enhancing navigation safety.

• The Plant Pathology Journal
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• v.36 no.5
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• pp.428-439
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• 2020

Erwinia pyrifoliae is a Gram-negative bacterial plant pathogen that causes black shoot blight in apple and pear. Although earlier studies reported the genome comparison of Erwinia species, E. pyrifoliae strains for such analysis were isolated in 1996. In 2014, the strain E. pyrifoliae EpK1/15 was newly isolated in the apple tree showing black shoot blight in South Korea. This study aimed to better understand the similarities and differences caused by natural variations at the genomic level between newly isolated E. pyrifoliae EpK1/15 and the strain Ep1/96, which were isolated almost 20 years apart. Several comparative genomic analyses were conducted, and Clusters of Orthologous Groups of proteins (COG) database was used to classify functional annotation for each strain. E. pyrifoliae EpK1/15 had similarities with the Ep1/96 strain in stress-related genes, Tn3 transposase of insertion sequences, type III secretion systems, and small RNAs. The most remarkable difference to emerge from this comparison was that although the draft genome of E. pyrifoliae EpK1/15 was almost conserved, Epk1/15 strain had at least three sorts of structural variations in functional annotation according to COG database; chromosome inversion, translocation, and duplication. These results indicate that E. pyrifoliae species has gone natural variations within almost 20 years at the genomic level, and we can trace their similarities and differences with comparative genomic analysis.

• Journal of Microbiology and Biotechnology
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• v.31 no.4
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• pp.601-609
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• 2021

Erythrobacter species are extensively studied marine bacteria that produce various carotenoids. Due to their photoheterotrophic ability, it has been suggested that they play a crucial role in marine ecosystems. It is essential to identify the genome sequence and the genes of the species to predict their role in the marine ecosystem. In this study, we report the complete genome sequence of the marine bacterium Erythrobacter sp. 3-20A1M. The genome size was 3.1 Mbp and its GC content was 64.8%. In total, 2998 genetic features were annotated, of which 2882 were annotated as functional coding genes. Using the genetic information of Erythrobacter sp. 3-20A1M, we performed pan-genome analysis with other Erythrobacter species. This revealed highly conserved secondary metabolite biosynthesis-related COG functions across Erythrobacter species. Through subsequent secondary metabolite biosynthetic gene cluster prediction and KEGG analysis, the carotenoid biosynthetic pathway was proven conserved in all Erythrobacter species, except for the spheroidene and spirilloxanthin pathways, which are only found in photosynthetic Erythrobacter species. The presence of virulence genes, especially the plant-algae cell wall degrading genes, revealed that Erythrobacter sp. 3-20A1M is a potential marine plant-algae scavenger.