Estimation of evolutionary average hydrophobicity profile from a family of protein sequences

Authors:
Said Hassan Ahmed;Tor Flå
Affiliations:
Dept of Mathematics and Statistics, University of Tromsø, Tromsø, Norway;Dept of Mathematics and Statistics, University of Tromsø, Tromsø, Norway
Venue:
PRIB'07 Proceedings of the 2nd IAPR international conference on Pattern recognition in bioinformatics
Year:
2007

Citing 2
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Abstract

Hydrophobicity has long been considered as one of the primary driving forces in the folding of proteins. We discuss here the evolutionary average of the hydrophobicity profile in an aligned family of proteins and found a patchy mean hydrophobicity profile. This is in contrast to Bastolla et al (2005b) results for the large superfamily of globular proteins. The idea is to use singular value decomposition and cavity filtering in order to remove the eigensequences burried in the evolutionary noise.