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Removing redundancy in SWISS-PROT and TrEMBL.

C O'Donovan1, M J Martin, E Glemet

  • 1EMBL Outstation - The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. odonovan@ebi.ac.uk

Bioinformatics (Oxford, England)
|May 1, 1999
PubMed
Summary

We developed a strategy to identify and remove redundancy within and between the SWISS-PROT and TrEMBL protein sequence databases. This ensures data integrity and improves the quality of these vital bioinformatics resources.

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Area of Science:

  • Bioinformatics
  • Proteomics
  • Database Management

Background:

  • SWISS-PROT is a protein sequence database known for minimal redundancy.
  • TrEMBL was introduced to enhance SWISS-PROT's comprehensiveness.
  • The integration of TrEMBL introduced some redundancy into the combined dataset.

Purpose of the Study:

  • To develop a robust strategy for identifying redundancy within and between SWISS-PROT and TrEMBL.
  • To implement a method for the effective removal of identified redundant entries.
  • To maintain the integrity and quality of protein sequence data.

Main Methods:

  • Algorithm development for redundancy detection.
  • Comparative analysis of sequence entries across databases.
  • Data curation and filtering techniques.

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Main Results:

  • A novel strategy for identifying sequence redundancy was successfully developed.
  • The implemented strategy effectively pinpointed redundant entries within and between SWISS-PROT and TrEMBL.
  • A significant reduction in data redundancy was achieved.

Conclusions:

  • The developed strategy effectively addresses redundancy in protein sequence databases.
  • Minimal redundancy is a key feature of SWISS-PROT, enhanced by TrEMBL.
  • The removal of redundancy improves the utility of SWISS-PROT and TrEMBL for research.