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© Oxford University Press

CONRAD: a method for identification of variable and conserved regions within proteins by scale-space filtering

Günter Herrmann 1, Annemarie Schön 2, Ruth Brack-Werner 2 and Thomas Werner 3,*

1Institut für Medizinische Informatik und Systemforschung Ingolstädter Landstraße 1, D-85758 Oberschleißheim, Germany
2Institut für Molekulare Virologie Ingolstädter Landstraße 1, D-85758 Oberschleißheim, Germany
3Institut für Säugetiergenetik, GSF-Forschungs-zentrum für Umwelt und Gesundheit GmbH Ingolstädter Landstraße 1, D-85758 Oberschleißheim, Germany

* To whom correspondence should be addressed. E-mail:werner{at}gsf.de

Advanced sequencing techniques allow rapid deduction of individual amino acid sequences of highly related proteins. Due to their quasi-species nature, viral genomes (e.g. HIV-1) represent one of the most common sources of related proteins. Another example of related proteins are immunoglobulins. Local differences in amino acid conservation are useful indicators of potential domain structures and immunological or functional epitopes prior to structural analysis of proteins. Although variability indices can be calculated by several methods, delineation of boundaries between sequence stretches with similar variability indices is left to the user. We use algorithmic scale-space filtering for delineation of conserved and variable sequence stretches within a protein which is performed on an algorithmic basis avoiding arbitrary assignments. Our method correctly identified variable regions for the human immunoglobulin {lambda}-chain V-regions (subgroup I). Prediction of the variable regions of the HIV-1 gp120 env protein was in agreement with empirical derived definitions. These examples indicate that our method is useful for the regional assignment of protein variability solely on the basis of amino acid sequences.

Received on December 19, 1995; revised on May 22, 1996; accepted on May 22, 1996

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