Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

SRS--an indexing and retrieval tool for flat file data libraries

T Etzold1, P Argos

  • 1European Molecular Biology Laboratory, Heidelberg, Germany.

Computer Applications in the Biosciences : CABIOS
|February 1, 1993
PubMed
Summary

The Sequence Retrieval System (SRS) offers flexible indexing and retrieval for biological sequence databases like EMBL and SwissProt. It efficiently manages complex data structures and supports various formats for bioinformatics research.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Prediction of protein folding pathways: Bovine pancreatic trypsin inhibitor.

Cytotechnology·2012
Same author

Structural adaptation of enzymes to low temperatures.

Protein engineering·2001
Same author

Strain in protein structures as viewed through nonrotameric side chains: I. their position and interaction.

Proteins·1999
Same author

Strain in protein structures as viewed through nonrotameric side chains: II. effects upon ligand binding.

Proteins·1999
Same author

Recognizing very distant sequence relationships among proteins by family profile analysis.

Proteins·1999
Same author

DATABANKS - a catalogue database of molecular biology databases.

Trends in biochemical sciences·1999

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Information Science

Background:

  • Biological sequence databases (e.g., EMBL, SwissProt) contain vast amounts of information.
  • Managing and retrieving data from these flat-file formatted libraries presents significant challenges.
  • Existing systems may lack the flexibility to adapt to evolving data structures.

Purpose of the Study:

  • To introduce the Sequence Retrieval System (SRS), an indexing and retrieval system.
  • To address the need for flexible data management in biological sequence databases.
  • To facilitate efficient querying and data access for researchers.

Main Methods:

  • Developed SRS, an information indexing and retrieval system.
  • Designed a specialized language (ODD) for specifying library formats and data organization.

Related Experiment Videos

  • Implemented special indices to support subentity lists and hierarchical data fields.
  • Created a user interface with pull-down menus and windows for querying and inspection.
  • Ensured compatibility with various input/output formats, including GCG programs.

    • Main Results:

    • SRS effectively indexes and retrieves data from flat-file biological sequence libraries.
    • The system supports complex data structures like feature tables and taxonomic classifications.
    • The ODD language provides flexibility for defining and adapting to diverse library formats.
    • The user interface allows for convenient querying and data inspection.
    • SRS demonstrates strong adaptability to evolving data formats and integrates well with existing bioinformatics tools.

    Conclusions:

    • SRS provides a robust and flexible solution for managing and retrieving data from biological sequence databases.
    • Its design accommodates the dynamic nature of biological data and facilitates efficient research.
    • The system enhances accessibility and usability of critical bioinformatics resources.