title: ProtEST: protein multiple sequence alignments from expressed sequence tags.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  The ProtEST method is available as an Internet World Wide Web service http://barton.ebi.ac.uk/servers/protest.html+ ++ The Wise2 package for protein and genomic comparisons and the ProtESTWise script can be found at http://www.sanger.ac.uk/Software/Wise2
  
  
  BACKGROUND
  geoff@ebi.ac.uk
authors.affiliation: European Molecular Biology Laboratory Outstation, European Bioinformatics Institute, Cambridge, UK.
authors.forename: J A
authors.initials: JA
authors.lastname: Cuff
authors.forename: E
authors.initials: E
authors.lastname: Birney
authors.forename: M E
authors.initials: ME
authors.lastname: Clamp
authors.forename: G J
authors.initials: GJ
authors.lastname: Barton
mesh_terms: D000595:Amino Acid Sequence; D020224:Expressed Sequence Tags; D008969:Molecular Sequence Data; D014176:Protein Biosynthesis; D011506:Proteins / Q000032:analysis*; D016415:Sequence Alignment / Q000379:methods*
chemical_list: D011506:Proteins