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ProtEST: protein multiple sequence alignments from expressed sequence tags.

J A Cuff1, E Birney, M E Clamp

  • 1European Molecular Biology Laboratory Outstation, European Bioinformatics Institute, Cambridge, UK.

Bioinformatics (Oxford, England)
|June 8, 2000
PubMed
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ProtEST is an automated method for creating protein sequence alignments from protein sequences and expressed sequence tags (ESTs). This approach enhances sequence data quality and improves protein secondary structure prediction accuracy.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Automated protein sequence alignment is crucial for understanding protein function and evolution.
  • Expressed Sequence Tags (ESTs) provide valuable, albeit often noisy, sequence data.

Purpose of the Study:

  • To introduce and evaluate ProtEST, an automated method for generating multiple protein sequence alignments from protein sequences and translated ESTs.
  • To demonstrate ProtEST's superiority over simple TBLASTN searches for EST database analysis.

Main Methods:

  • ProtEST automatically clusters, assembles, and de-redundantizes sequences.
  • Sequences undergo error checking and translation into protein before alignment.
  • The method is available as a web service and via the Wise2 package.

Related Experiment Videos

Main Results:

  • ProtEST identified corrected EST sequences for over 58% of probes from Pfam-A seed alignments.
  • Resulting alignments of translated EST sequences averaged over 10 sequences per family.
  • Protein secondary structure prediction accuracy improved by 3.4% using ProtEST alignments compared to single sequences.

Conclusions:

  • ProtEST offers a robust and automated solution for processing and aligning EST data.
  • The method significantly enhances the quality of sequence alignments and downstream analyses like structure prediction.