VaProS: a database-integration approach for protein/genome information retrieval

Takashi Gojobori, Kazuho Ikeo, Yukie Katayama, Takeshi Kawabata, Akira R. Kinjo, Kengo Kinoshita, Yeondae Kwon, Ohsuke Migita, Hisashi Mizutani, Masafumi Muraoka, Koji Nagata, Satoshi Omori, Hideaki Sugawara, Daichi Yamada, Kei Yura

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

Life science research now heavily relies on all sorts of databases for genome sequences, transcription, protein three-dimensional (3D) structures, protein–protein interactions, phenotypes and so forth. The knowledge accumulated by all the omics research is so vast that a computer-aided search of data is now a prerequisite for starting a new study. In addition, a combinatory search throughout these databases has a chance to extract new ideas and new hypotheses that can be examined by wet-lab experiments. By virtually integrating the related databases on the Internet, we have built a new web application that facilitates life science researchers for retrieving experts’ knowledge stored in the databases and for building a new hypothesis of the research target. This web application, named VaProS, puts stress on the interconnection between the functional information of genome sequences and protein 3D structures, such as structural effect of the gene mutation. In this manuscript, we present the notion of VaProS, the databases and tools that can be accessed without any knowledge of database locations and data formats, and the power of search exemplified in quest of the molecular mechanisms of lysosomal storage disease. VaProS can be freely accessed at http://p4d-info.nig.ac.jp/vapros/.

Original languageEnglish
Pages (from-to)69-81
Number of pages13
JournalJournal of Structural and Functional Genomics
Volume17
Issue number4
DOIs
Publication statusPublished - 2016 Dec 1
Externally publishedYes

Fingerprint

Information Storage and Retrieval
Information retrieval
Genes
Genome
Databases
Proteins
Biological Science Disciplines
Research
Lysosomal Storage Diseases
Transcription
Internet
Research Personnel
Phenotype
Mutation
Experiments

Keywords

  • Big data analysis
  • Database integration
  • Lysosomal storage disease
  • Protein 3D structure

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Genetics

Cite this

VaProS : a database-integration approach for protein/genome information retrieval. / Gojobori, Takashi; Ikeo, Kazuho; Katayama, Yukie; Kawabata, Takeshi; Kinjo, Akira R.; Kinoshita, Kengo; Kwon, Yeondae; Migita, Ohsuke; Mizutani, Hisashi; Muraoka, Masafumi; Nagata, Koji; Omori, Satoshi; Sugawara, Hideaki; Yamada, Daichi; Yura, Kei.

In: Journal of Structural and Functional Genomics, Vol. 17, No. 4, 01.12.2016, p. 69-81.

Research output: Contribution to journalArticle

Gojobori, T, Ikeo, K, Katayama, Y, Kawabata, T, Kinjo, AR, Kinoshita, K, Kwon, Y, Migita, O, Mizutani, H, Muraoka, M, Nagata, K, Omori, S, Sugawara, H, Yamada, D & Yura, K 2016, 'VaProS: a database-integration approach for protein/genome information retrieval', Journal of Structural and Functional Genomics, vol. 17, no. 4, pp. 69-81. https://doi.org/10.1007/s10969-016-9211-3
Gojobori, Takashi ; Ikeo, Kazuho ; Katayama, Yukie ; Kawabata, Takeshi ; Kinjo, Akira R. ; Kinoshita, Kengo ; Kwon, Yeondae ; Migita, Ohsuke ; Mizutani, Hisashi ; Muraoka, Masafumi ; Nagata, Koji ; Omori, Satoshi ; Sugawara, Hideaki ; Yamada, Daichi ; Yura, Kei. / VaProS : a database-integration approach for protein/genome information retrieval. In: Journal of Structural and Functional Genomics. 2016 ; Vol. 17, No. 4. pp. 69-81.
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