ProtEST: protein multiple sequence alignments from expressed sequence tags

J A Cuff, E Birney, M E Clamp, G J Barton

Research output: Contribution to journalArticlepeer-review

13 Citations (Scopus)


MOTIVATION: An automatic sequence searching method (ProtEST) is described which constructs multiple protein sequence alignments from protein sequences and translated expressed sequence tags (ESTs). ProtEST is more effective than a simple TBLASTN search of the query against the EST database, as the sequences are automatically clustered, assembled, made non-redundant, checked for sequence errors, translated into protein and then aligned and displayed.

RESULTS: A ProtEST search found a non-redundant, translated, error- and length-corrected EST sequence for > 58% of sequences when single sequences from 1407 Pfam-A seed alignments were used as the probe. The average family size of the resulting alignments of translated EST sequences contained > 10 sequences. In a cross-validated test of protein secondary structure prediction, alignments from the new procedure led to an improvement of 3.4% average Q3 prediction accuracy over single sequences.

AVAILABILITY: The ProtEST method is available as an Internet World Wide Web service ++ The Wise2 package for protein and genomic comparisons and the ProtESTWise script can be found at


Original languageEnglish
Pages (from-to)111-6
Number of pages6
Issue number2
Publication statusPublished - Feb 2000


  • Amino Acid Sequence
  • Expressed Sequence Tags
  • Molecular Sequence Data
  • Protein Biosynthesis
  • Proteins
  • Sequence Alignment


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