Protein Engineering, Vol. 12, No. 5, 387-394,
May 1999
© 1999 Oxford University Press
PSIC: profile extraction from sequence alignments with position-specific counts of independent observations
1 European Molecular Biology Laboratory, Meyerhofstrasse1, Postfach 10.2209, D-69012 Heidelberg, 2 Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Strasse 10, D-13122 Berlin-Buch, Germany, 3 V.A. Engelhardt Institut of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, 117984 Moscow, 5 Moscow Institute of Physics and Technology, Institutsky per. 9, Dolgoprudny, Moscow Region and 6 Institute of Control Sciences, Russian Academy of Sciences, Profsoyuznaya Street 65, 117806 Moscow, Russia
Sequence weighting techniques are aimed at balancing redundant observed information from subsets of similar sequences in multiple alignments. Traditional approaches apply the same weight to all positions of a given sequence, hence equal efficiency of phylogenetic changes is assumed along the whole sequence. This restrictive assumption is not required for the new method PSIC (position-specific independent counts) described in this paper. The number of independent observations (counts) of an amino acid type at a given alignment position is calculated from the overall similarity of the sequences that share the amino acid type at this position with the help of statistical concepts. This approach allows the fast computation of position-specific sequence weights even for alignments containing hundreds of sequences. The PSIC approach has been applied to profile extraction and to the fold family assignment of protein sequences with known structures. Our method was shown to be very productive in finding distantly related sequences and more powerful than Hidden Markov Models or the profile methods in WiseTools and PSI-BLAST in many cases. The profile extraction routine is available on the WWW (http://www.bork.embl-heidelberg.de/PSIC or http://www.imb.ac.ru/PSIC).
Keywords: fold recognition/motif recognition/profile extraction/position-specific independent counts/PSIC/sequence weighting
4 To whom correspondence should be addressed. E-mail frank.eisenhaber{at}embl-heidelberg.de
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