ProtEST: protein multiple sequence alignments from expressed sequence tags

TY - JOUR

T1 - ProtEST

T2 - protein multiple sequence alignments from expressed sequence tags

AU - Cuff, J A

AU - Birney, E

AU - Clamp, M E

AU - Barton, G J

PY - 2000/2

Y1 - 2000/2

N2 - 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/Wise2CONTACT: [email protected]

AB - 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/Wise2CONTACT: [email protected]

KW - Amino Acid Sequence

KW - Expressed Sequence Tags

KW - Molecular Sequence Data

KW - Protein Biosynthesis

KW - Proteins

KW - Sequence Alignment

U2 - 10.1093/bioinformatics/16.2.111

DO - 10.1093/bioinformatics/16.2.111

M3 - Article

C2 - 10842731

SN - 1367-4803

VL - 16

SP - 111

EP - 116

JO - Bioinformatics

JF - Bioinformatics

IS - 2

ER -