Sturgeon aqua-cultured in Korea is mainly Acipenser ruthenus and its culture began in the early 2000's. In this study, Carnobacterium sp. was isolated from unprocessed caviar of aqua-cultured Acipenser ruthenus. The 16s rRNA nucleotide sequence obtained from Carnobacterium sp. isolate (accession no. KM236206) was deposited with GenBank and homologous with Carnobacterium divergens DSM 20623 and NBRC15683 strain. In conclusion, this is first report of isolation of Carnobacterium sp. from caviar of Acipenser ruthenus aqua-cultured in Korea. In the future, it must be ascertained whether Carnobacterium sp. degenerate of caviar or cause diseases in sturgeon.
Base Sequence ; Carnobacterium* ; Databases, Nucleic Acid ; Korea

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.
Abstracting and Indexing as Topic ; Databases, Nucleic Acid ; Databases, Protein

Mining interesting patterns from DNA sequences is one of the most challenging tasks in bioinformatics and computational biology. Maximal contiguous frequent patterns are preferable for expressing the function and structure of DNA sequences and hence can capture the common data characteristics among related sequences. Biologists are interested in finding frequent orderly arrangements of motifs that are responsible for similar expression of a group of genes. In order to reduce mining time and complexity, however, most existing sequence mining algorithms either focus on finding short DNA sequences or require explicit specification of sequence lengths in advance. The challenge is to find longer sequences without specifying sequence lengths in advance. In this paper, we propose an efficient approach to mining maximal contiguous frequent patterns from large DNA sequence datasets. The experimental results show that our proposed approach is memory-efficient and mines maximal contiguous frequent patterns within a reasonable time.
Base Sequence ; Computational Biology ; Databases, Nucleic Acid ; DNA ; Mining

OBJECTIVETo predict orthologous sequences of the GENCODE-identified 13 562 human long non-coding RNAs (lncRNA) in 16 mammalian genomes and construct a lncRNA database LongMan for lncRNA studies.

METHODSThe exon structures of a total of 13 562 human lncRNAs were analyzed using RNAfold, and their orthologous sequences were searched against 16 mammalian genomes using Infernal. The potential orthologous genes, transposons and splicing signals of human lncRNAs were predicted to construct a lncRNA database with a updating mechanism.

RESULTSand

CONCLUSIONThe lncRNA database LongMan we constructed, which currently contains 133 646 orthologous lncRNAs, provides information of the sequences, alignments, transposons, and species-specific insertions and deletions and allows database search on combinatorial conditions, graphic display and data download. As the first large-scale mammalian orthologous lncRNA database, LongMan has important values in future comparative and functional studies of lncRNAs.

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.
Computational Biology ; Databases, Nucleic Acid ; Formycins ; Organothiophosphorus Compounds ; Ribonucleotides

Although abundant biology data have been accumulated in public biology databases, such as GenBank and PIR, few easy-interface services are provided for users to access or update them. We have developed a system, named BioStore, that is composed of several programs to aid users to not only access public data but also share their own data easily. The service can be used for maintaining a local database as a repository of raw data files of several public databases and distributing the data files to other users. Currently, BioStore manipulates major bio-databases and will expand to include more databases and more useful interfaces.
Biology ; Databases, Nucleic Acid ; Formycins ; Ribonucleotides ; Information Storage and Retrieval

Recently, the Fusarium genus has been narrowed based upon phylogenetic analyses and a Fusarium-like clade was adopted. The few species of the Fusarium-like clade were moved to new, re-installed or existing genera or provisionally retained as "Fusarium." Only a limited number of reference strains and DNA marker sequences are available for this clade and not much is known about its actual species diversity. Here, we report six strains, preserved by the Belgian fungal culture collection BCCM/IHEM as a Fusarium species, that belong to the Fusarium-like clade. They showed a slow growth and produced pionnotes, typical morphological characteristics of many Fusarium-like species. Multilocus sequencing with comparative sequence analyses in GenBank and phylogenetic analyses, using reference sequences of type material, confirmed that they were indeed member of the Fusarium-like clade. One strain was identified as "Fusarium" ciliatum whereas another strain was identified as Fusicolla merismoides. The four remaining strains were shown to represent a unique phylogenetic lineage in the Fusarium-like clade and were also found morphologically distinct from other members of the Fusarium-like clade. Based upon phylogenetic considerations, a new genus, Pseudofusicolla gen. nov., and a new species, Pseudofusicolla belgica sp. nov., were installed for this lineage. A formal description is provided in this study. Additional sampling will be required to gather isolates other than the historical strains presented in the present study as well as to further reveal the actual species diversity in the Fusarium-like clade.
Databases, Nucleic Acid ; Fusarium ; Genetic Markers ; Phylogeny ; Sequence Analysis

Along with the rapid research of neural molecular biology, abundant data are produced so that the collection and coordination of high-throughout data about nervous system relative proteins and genes are imperative. Through analyzing the biological primary databases maintained by NCBI and RCSB as the main data source and designing a new data model, a local specialized secondary database is constructed, which mainly includes nucleotide sequences, protein sequences and protein structures, and is established on Sun Blade 2000 System and Oracle 9i. All programs are developed by Java technology. A method of web information automatic retrieval with XML is proposed for sequence data collection and submission to the database. JSP + JavaBean technology is used to support data promulgation on Internet. The establishment of this database provides an excellent platform for the research of neural molecular biology and the pathogenesis of related diseases.
Database Management Systems ; Databases, Nucleic Acid ; Databases, Protein ; Gene Expression Profiling ; Humans ; Nervous System ; Proteins ; chemistry

The spike gene of porcine epidemic diarrhea virus (PEDV) was sequenced from 55 South China field strains isolated from pigs with symptoms of diarrhea. The sequences were compared within the set of field strains as well as with reference strains available in GenBank. Within the 55 South China PEDV field strains, the deduced amino acid sequence identities ranged from 93.8% to 99.9 % and ranged from 90.7% to 99.5% when compared with the foreign reference strains in GenBank. Our phylogenetic analysis showed that 10 of the 55 South China PEDV strains belonged to G1b and 45 belonged to G2b.
Amino Acid Sequence ; China* ; Databases, Nucleic Acid ; Diarrhea ; Porcine epidemic diarrhea virus* ; Sequence Analysis* ; Swine

BACKGROUND: Accurate and rapid identification of pathogens is one of the most important tasks of the clinical microbiology laboratory, and, in cases of rare pathogens, the identification is difficult and time-consuming upon the use of conventional methods alone. Herein, we will report our molecular work involving the identification of bacteria and fungi. METHODS: Sixty bacterial isolates had been collected from November 2004 to May 2007, and 15 fungal isolates had been collected from September 2005 to May 2007. Species identifications were performed using sequence analyses of the 16S rRNA region of bacteria and the internal transcribed spacer (ITS) region of fungi. The data were compared with those of GenBank (http://www.ncbi.nlm.nih.gov/) or EMBL (http://www.ebi.ac.uk/embl/). RESULTS: Sixty bacterial isolates included: 23 isolates with genus information (group 1), 17 isolates (group 2) that were too fastidious for genus or species identification, 16 isolates (group 3) with results from identification kits having low confidence, and 4 isolates (group 4) with odd antibiograms according to the species. In 58 of 60 isolates, identification of the genus or species could be obtained using molecular genetic methods. Thirty-eight isolates (63%) and 20 (33%) of 58 isolates could be identified at the species and genus levels, repectively. Among the total of 15 fungal isolates, 11 (73%) and 4 (27%) isolates were identified at the species and genus levels, respectively. CONCLUSION: 16S rRNA and ITS sequencing analyses are very useful for identifying the species or genus of a pathogenic microorganism in the clinical microbiology laboratory.
Bacteria ; Base Sequence ; Databases, Nucleic Acid ; Fungi ; Microbial Sensitivity Tests ; Molecular Biology ; Sequence Analysis