• Proceedings of the Korean Society of Plant Pathology Conference
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• 2002.09a
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• pp.196.1-196
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• 2002

• Genomics & Informatics
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• v.7 no.3
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• pp.175-177
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• 2009

We have developed WinBioDBs with Windows interfaces, which include importing modules and searching interfaces for 10 major public databases such as GenBank, PIR, SwissProt, Pathway, EPD, ENZYME, REBASE, Prosite, Blocks, and Pfam. User databases can be constructed with searching results of queries and their entries can be edited. The program is a stand-alone database searching program on Windows PC. Database update features are supported by importing raw database files and indexing after downloading them. Users can adjust their own searching environments and report format and construct their own projects consisting of a combination of a local databases. WinBioDBs are implemented with VC++ and its database is based on MySQL.

• BMB Reports
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• v.40 no.2
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• pp.286-289
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• 2007

Despite considerable interest in the biologic processes of regeneration and stem cell activation, little is known about the genes involved in these transformative events. In a Hydra littoralis model of regeneration, we employed a rapid shotgun suppression subtractive hybridization strategy to identify genes that are uniquely expressed in regenerating tissue. With an adaptor-PCR based technique, 16 candidate transcripts were identified, 15 were confirmed unique to mRNA isolated from hydra undergoing regeneration. Of these, 6 were undescribed in GenBank and allied expressed sequence tag (EST) databases (GenBank + EMBL + DDBJ + PDB and the Hydra EST database). BLAST analysis of these sequences identified remarkably similar sequences in anonymous ESTs found in a wide variety of animal species.

• BMB Reports
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• v.35 no.5
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• pp.513-517
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• 2002

We describe a new method for identifying the sequences that signal the start of translation, and the boundaries between exons and introns (donor and acceptor sites) in human mRNA. According to the mandatory keyword, ORGANISM, and feature key, CDS, a large set of standard data for each signal site was extracted from the ASCII flat file, gbpri.seq, in the GenBank release 108.0. This was used to generate the scoring matrices, which summarize the sequence information for each signal site. The scoring matrices take into account the independent nucleotide frequencies between adjacent bases in each position within the signal site regions, and the relative weight on each nucleotide in proportion to their probabilities in the known signal sites. Using a scoring scheme that is based on the nucleotide scoring matrices, the method has great sensitivity and specificity when used to locate signals in uncharacterized human genomic DNA. These matrices are especially effective at distinguishing true and false sites.

• The Plant Pathology Journal
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• v.22 no.4
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• pp.334-338
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• 2006

Chrysanthemum chlorotic mottle viroid(CChMVd) isolates have been identified from chrysanthemum showing yellow spots or infected without symptom. They were 399-400 nucleotides length of RNA. CChMVd-SSHA6(GenBank accession no. DQ450682) revealed a GAAA to DUUC substitution in positions 82-85 of CChMVd-MSIN34(GenBank accession no. DQ402041). In vitro RNA transcripts with the complete CChMVd sequence were infectious and induced the typical CChMVd infection symptom of yellow spots in chrysanthemum cv. Sharotte. CChMVd caused reduction in growth in some cultivars, whereas some cultivars were not affected. This is the first report on the occurrence of CChMVd in chrysanthemum in Korea.

• International Journal of Industrial Entomology and Biomaterials
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• v.15 no.2
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• pp.115-122
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• 2007

As the genome of B.mori is available in GenBank and the EST database of B.mori is expanding, identification of novel genes of B.mori is conceivable by data-mining techniques. We used the in silico cloning method to get the vacuolar-type $H^+-ATP$ synthetase (V-ATPase) c subunit (16 kDa proteolipid subunit) gene of B.mori and analysed with bioinformatics tools. The result was confirmed by RT-PCR and sequencing. The V-ATPase c subunit cDNA contains a 468 bp ORF. The ORF encoded a 155-residue protein that showed extensive homology with V-ATPase c subunits from other 15 species and contained four membrane-spanning helices. Tissue expression pattern analysis revealed that V-ATPase c expressed strongly in Malpighian tubules, not in fat body. This gene has been registered in GenBank under the accession number EU082222.

• Animal Systematics, Evolution and Diversity
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• v.28 no.3
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• pp.178-184
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• 2012

Echinoids were collected at depths of 5-10 m in Munseom, Jeju Island by SCUBA diving on November 23, 2008 and September 15, 2009. Two specimens were identified as Echinometra mathaei (Blainville, 1825) based on morphological characteristics and molecular analyses of mitochondrial cytochrome c oxidase subunit I partial sequences. Echinometra mathaei collected from Korea was redescribed with photographs and was compared with other species from GenBank based on molecular data. Phylogenetic analyses showed that no significant differences were between base sequences of E. mathaei from Korea and that from GenBank. To date, 13 echinoids including this species have been reported from Jeju Island, and 32 echinoids have been recorded in Korea.

• The Plant Pathology Journal
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• v.24 no.3
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• pp.305-308
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• 2008

A viroid was detected from symptomless Coleus blumei cultivar 'Kong Scarlet'. It consisted of 249 nucleotides(GenBank accession no. EU410620), which was 100% identical to a Coleus blumei viroid 1(CbVd 1) reported from China(GenBank accession no. DQI78399), indicating that the viroid was an isolate of CbVd1. Attempts were made to determine if commercial Coleus seeds were infected with CbVd. Infection rates in seedlings of the 14 commercial cultivars of Coleus ranged from 0 to 100%. CbVd1 caused discoloration and growth retardation in some cultivars, but is symptomless in others. These results indicated that Coleus in commercial markets in Korea is highly infected with CbVd.

• Genomics & Informatics
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• v.6 no.2
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• pp.95-97
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• 2008

Many bioinformatics sites have managed local bio-databases, including major databases such as GenBank and PIR with update load. We have developed several programs to monitor the update status of these databases and to FTP them automatically. These programs can be used for maintaining local bio-databases as recent versions and providing up-to-date databases through FTP sites. Currently, the program serves major bio-databases and will extend to accommodate many more bio-databases.

• Journal of fish pathology
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• v.16 no.2
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• pp.125-129
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• 2003

Conncxin (Cx) is an important and essential protein induction of oocyte maturation, which is present in almost all mammalian tissucs except cirulating blood cells and adult skeletal museles. In this study, goldfish Cx43 cDNA sequence is available in GenBank under the accession number AB078505. Homology analyses using the GenBank and EMBL general database searches indicated that goldfish Cx43 cDNA has a high homology with carp Cx43 (95.1% identity), zebrafish Cx43 (90.5% identity), and chicken Cx43 (81.9% identity). Goldfish Cx43 is similar to the Cx family in its general features, and all the typical Cx consensus sequences are also found. Moreover, significantly increased Cx43 transcrpts were observed in mature goldfish (GSI; 18.3-21.7) pituitary and ovary when compared with immature goldfish (GSI; 4.9-6.0). Cx43 transeripts were weakly detectrd in both liver and kidney of immature and mature goldfish. There is possible that Cx43 nctivity was relation to oocyte maturation in the goldfish.