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SeqHound: biological sequence and structure database as a platform for bioinformatics research.

Katerina Michalickova1, Gary D Bader, Michel Dumontier

  • 1Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8. katerina@mshri.on.ca

BMC Bioinformatics
|October 29, 2002
PubMed
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SeqHound is a bioinformatics database system integrating sequence, taxonomy, annotation, and 3-D structure data. It provides a high-performance, locally-hosted platform for research, offering daily updated content and flexible data retrieval options.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • SeqHound is an integrated database system for biological sequences, taxonomy, annotation, and 3-D structures.
  • It offers a high-performance, locally-hosted server platform tailored for bioinformatics research.

Purpose of the Study:

  • To present SeqHound, a comprehensive database system for biological data.
  • To highlight its utility in managing and retrieving diverse biological information.

Main Methods:

  • Based on the National Center for Biotechnology Information (NCBI) data model and tools.
  • Utilizes a web server with remote APIs (Perl, C, C++) and an optimized local API.
  • Provides functionality for retrieving specialized subsets of sequences, structures, and domains.

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Main Results:

  • Offers daily updated Entrez sequence databases, 3-D structural data, and associated information (redundancies, neighbors, taxonomy, annotations, literature links).
  • Supports retrieval of sequences in FASTA, GenBank, ASN.1, and XML formats; structures in ASN.1, XML, and PDB formats.
  • Emphasizes complete genomes, taxonomy, domain/functional annotation, and 3-D structural data retrieval via API.

Conclusions:

  • SeqHound has proven valuable in bioinformatics projects (e.g., BIND database) and offers a cost-effective research infrastructure.
  • The system will continue development as a service of the Blueprint Initiative.
  • Source code and examples are available under the GNU public license on Sourceforge.