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IDBD: infectious disease biomarker database.

Yang IS, Ryu C, Cho KJ, Kim JK, Ong SH, Mitchell WP, Kim BS, Oh HB, Kim KH - Nucleic Acids Res. (2007)

Bottom Line: Despite intensified interest and research, however, the overall rate of development of novel biomarkers has been falling.IDBD is a community annotation database, utilizing collaborative Web 2.0 features, providing a convenient user interface to input and revise data online.It supports various types of data searches and application tools to analyze sequence and structure features of potential and validated biomarkers.

View Article: PubMed Central - PubMed

Affiliation: Department of Life Sciences & Biotechnology, School of Life Sciences & Biotechnology, Korea University, Seoul, Korea.

ABSTRACT
Biomarkers enable early diagnosis, guide molecularly targeted therapy and monitor the activity and therapeutic responses across a variety of diseases. Despite intensified interest and research, however, the overall rate of development of novel biomarkers has been falling. Moreover, no solution is yet available that efficiently retrieves and processes biomarker information pertaining to infectious diseases. Infectious Disease Biomarker Database (IDBD) is one of the first efforts to build an easily accessible and comprehensive literature-derived database covering known infectious disease biomarkers. IDBD is a community annotation database, utilizing collaborative Web 2.0 features, providing a convenient user interface to input and revise data online. It allows users to link infectious diseases or pathogens to protein, gene or carbohydrate biomarkers through the use of search tools. It supports various types of data searches and application tools to analyze sequence and structure features of potential and validated biomarkers. Currently, IDBD integrates 611 biomarkers for 66 infectious diseases and 70 pathogens. It is publicly accessible at http://biomarker.cdc.go.kr and http://biomarker.korea.ac.kr.

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Related in: MedlinePlus

The sequence and structure analysis tools showing (A) analysis results using selected sequences of biomarker data: sequence alignment and phylogenetic tree, and (B) predicted 3D structure of a biomarker viewed with Jmol.
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Figure 3: The sequence and structure analysis tools showing (A) analysis results using selected sequences of biomarker data: sequence alignment and phylogenetic tree, and (B) predicted 3D structure of a biomarker viewed with Jmol.

Mentions: On the biomarker list page, IDBD allows access to sequence and structure analysis tools by clicking ‘Data analysis new window’ on the left-hand navigation bar. The user can select sequences of interest obtained from biomarker search (Figure 1E), prepare an input data by clicking ‘Sequence alignment’, and conduct multiple sequence alignment by direct submission or upload a file of the chosen sequences to CLUSTALW tool of EBI (16). On the result page (Figure 3A), the alignment can then be exported for phylogenetic tree construction. The sequence analysis also includes standard BLAST services (blastn and blastp) on external network connectivity (17), pairwise distance and synonymous—non-synonymous ratio analysis. In the case of structure analysis, users may submit an amino acid sequence or multiple sequences aligned to a set of methods for secondary (PSA) and tertiary structure (Geno3d) prediction (18,19). The predicted tertiary structures can be modeled by using Jmol either with a PDB file or PDB ID, if available (Figure 3B).Figure 3.


IDBD: infectious disease biomarker database.

Yang IS, Ryu C, Cho KJ, Kim JK, Ong SH, Mitchell WP, Kim BS, Oh HB, Kim KH - Nucleic Acids Res. (2007)

The sequence and structure analysis tools showing (A) analysis results using selected sequences of biomarker data: sequence alignment and phylogenetic tree, and (B) predicted 3D structure of a biomarker viewed with Jmol.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238845&req=5

Figure 3: The sequence and structure analysis tools showing (A) analysis results using selected sequences of biomarker data: sequence alignment and phylogenetic tree, and (B) predicted 3D structure of a biomarker viewed with Jmol.
Mentions: On the biomarker list page, IDBD allows access to sequence and structure analysis tools by clicking ‘Data analysis new window’ on the left-hand navigation bar. The user can select sequences of interest obtained from biomarker search (Figure 1E), prepare an input data by clicking ‘Sequence alignment’, and conduct multiple sequence alignment by direct submission or upload a file of the chosen sequences to CLUSTALW tool of EBI (16). On the result page (Figure 3A), the alignment can then be exported for phylogenetic tree construction. The sequence analysis also includes standard BLAST services (blastn and blastp) on external network connectivity (17), pairwise distance and synonymous—non-synonymous ratio analysis. In the case of structure analysis, users may submit an amino acid sequence or multiple sequences aligned to a set of methods for secondary (PSA) and tertiary structure (Geno3d) prediction (18,19). The predicted tertiary structures can be modeled by using Jmol either with a PDB file or PDB ID, if available (Figure 3B).Figure 3.

Bottom Line: Despite intensified interest and research, however, the overall rate of development of novel biomarkers has been falling.IDBD is a community annotation database, utilizing collaborative Web 2.0 features, providing a convenient user interface to input and revise data online.It supports various types of data searches and application tools to analyze sequence and structure features of potential and validated biomarkers.

View Article: PubMed Central - PubMed

Affiliation: Department of Life Sciences & Biotechnology, School of Life Sciences & Biotechnology, Korea University, Seoul, Korea.

ABSTRACT
Biomarkers enable early diagnosis, guide molecularly targeted therapy and monitor the activity and therapeutic responses across a variety of diseases. Despite intensified interest and research, however, the overall rate of development of novel biomarkers has been falling. Moreover, no solution is yet available that efficiently retrieves and processes biomarker information pertaining to infectious diseases. Infectious Disease Biomarker Database (IDBD) is one of the first efforts to build an easily accessible and comprehensive literature-derived database covering known infectious disease biomarkers. IDBD is a community annotation database, utilizing collaborative Web 2.0 features, providing a convenient user interface to input and revise data online. It allows users to link infectious diseases or pathogens to protein, gene or carbohydrate biomarkers through the use of search tools. It supports various types of data searches and application tools to analyze sequence and structure features of potential and validated biomarkers. Currently, IDBD integrates 611 biomarkers for 66 infectious diseases and 70 pathogens. It is publicly accessible at http://biomarker.cdc.go.kr and http://biomarker.korea.ac.kr.

Show MeSH
Related in: MedlinePlus