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Related Experiment Videos

FramePlus: aligning DNA to protein sequences.

E Halperin1, S Faigler, R Gill-More

  • 1Compugen Ltd., Tel Aviv, Israel.

Bioinformatics (Oxford, England)
|April 1, 2000
PubMed
Summary
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A new algorithm, FramePlus, improves DNA-protein sequence alignment for automated annotation of Expressed Sequence Tags (ESTs). It shows better performance with frameshift errors, aiding in large database searches.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Automated annotation of Expressed Sequence Tags (ESTs) is crucial due to rapidly growing databases.
  • Sequence alignment algorithms are key to successful EST annotation.
  • Current methods face challenges with sequencing errors and frameshifts.

Purpose of the Study:

  • Introduce FramePlus, a novel algorithm for DNA-protein sequence alignment.
  • Develop a general framework for testing alignment algorithm sensitivity using the SCOP database.
  • Evaluate FramePlus performance against existing algorithms.

Main Methods:

  • Developed a novel DNA-protein sequence alignment algorithm named FramePlus.
  • Utilized the SCOP database to create a sensitivity testing framework.

Related Experiment Videos

  • Compared FramePlus performance with other alignment algorithms under various error conditions.

    • Main Results:

    • FramePlus demonstrates superior performance over other algorithms with moderate to high frameshift errors.
    • FramePlus shows comparable performance to Translated Search when sequencing errors are absent.
    • The developed framework allows for robust evaluation of alignment algorithm sensitivity.

    Conclusions:

    • FramePlus offers an effective solution for DNA-protein sequence alignment, particularly in the presence of frameshift errors.
    • The sensitivity testing framework provides a valuable tool for assessing alignment algorithm performance.
    • FramePlus enhances the accuracy of automated EST annotation in large-scale genomic studies.