Dresden 2009 – scientific programme

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BP: Fachverband Biologische Physik

BP 5: Proteins

BP 5.8: Talk

Monday, March 23, 2009, 16:30–16:45, ZEU 260

High Quality Protein Sequence Alignment combining Structural Profile Prediction and Structural Profile Alignment with SABERTOOTH — Florian Teichert¹, •Jonas Minning¹, Ugo Bastolla², and Markus Porto¹ — ¹Institut für Festkörperphysik, Technische Universität Darmstadt, Germany — ²Centro de Biología Molecular ‘Severo Ochoa’, CSIC-UAM, Madrid, Spain

To discover evolutionary and functional relationships between proteins by alignment is a major issue in various fields. In many cases, protein structures are not known and one has to rely on aligning protein sequences. Here, we combine (i) a recently developed ansatz to predict structural profiles from sequence with (ii) our structural alignment algorithm SABERTOOTH which is based on structural profiles [1]. Comparing the performance of the resulting sequence alignment algorithm with established tools, we prove a significantly higher quality of the determined alignments evaluated from a structural point of view.

[1] F. Teichert, U. Bastolla, and M. Porto, BMC Bioinformatics 8, 425 (2007)