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Support for BioIndexing in BLASTgres

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Data Integration in the Life Sciences (DILS 2005)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 3615))

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Abstract

The ability to perform genome-wide and cross-genome data analyses can dramatically reduce the time required for new biological discoveries. This raises important issues in bioinformatics database research involving data representations and data integration. Essential biodatatypes (biological datatypes such as sequence locations) and tools (such as the popular BLAST sequence alignment tools) are not supported in traditional database systems, which has forced researchers to represent biological knowledge counterintuitively, and implement codes for data operations. This paper introducesBLASTgres, an extension of the PostgreSQL database system, that provides indexable biodatatypes and joinable BLAST alignment.

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References

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Author information

Authors and Affiliations

  1. Computer Science Department, University of California, Los Angeles, CA, 90095-1596, USA

    Ruey-Lung Hsiao, D. Stott Parker & Hung-chih Yang

Authors
  1. Ruey-Lung Hsiao
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  2. D. Stott Parker
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  3. Hung-chih Yang
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Editor information

Editors and Affiliations

  1. Department of Computer Science, University of California, Davis,  

    Bertram Ludäscher

  2. University of Maryland, College Park, 20742, MD, USA

    Louiqa Raschid

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© 2005 Springer-Verlag Berlin Heidelberg

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Hsiao, RL., Parker, D.S., Yang, Hc. (2005). Support for BioIndexing in BLASTgres. In: Ludäscher, B., Raschid, L. (eds) Data Integration in the Life Sciences. DILS 2005. Lecture Notes in Computer Science(), vol 3615. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11530084_23

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  • DOI: https://doi.org/10.1007/11530084_23

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-27967-9

  • Online ISBN: 978-3-540-31879-8

  • eBook Packages: Computer ScienceComputer Science (R0)

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