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Bioinformatics Vol. 16 no. 2 2000
Pages 111-116
© 2000 Oxford University Press

ProtEST: protein multiple sequence alignments from expressed sequence tags

James A. Cuff 1,2, Ewan Birney 3, Michele E. Clamp 2 and Geoffrey J. Barton 2

1 Laboratory of Molecular Biophysics, Rex Richards Building, South Parks Road, Oxford OX1 3QU
2 European Molecular Biology Laboratory Outstation – European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD
3 The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

Present address: The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

To whom correspondence should be addressed.

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 at http://barton.ebi.ac.uk/servers/protest.htmlThe Wise2 package for protein and genomic comparisons and the ProtESTWise script can be found at: http://www.sanger.ac.uk/Software/Wise2

Contact: geoff{at}ebi.ac.uk

Received on June 4, 1999 ; revised on August 16, 1999 ; accepted on August 25, 1999

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