ProtEST: protein multiple sequence alignments from expressed sequence tags

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 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 CONTACT [email protected]