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BMCBI
2006

On single and multiple models of protein families for the detection of remote sequence relationships

9 years 2 months ago
On single and multiple models of protein families for the detection of remote sequence relationships
Background: The detection of relationships between a protein sequence of unknown function and a sequence whose function has been characterised enables the transfer of functional annotation. However in many cases these relationships can not be identified easily from direct comparison of the two sequences. Methods which compare sequence profiles have been shown to improve the detection of these remote sequence relationships. However, the best method for building a profile of a known set of sequences has not been established. Here we examine how the type of profile built affects its performance, both in detecting remote homologs and in the resulting alignment accuracy. In particular, we consider whether it is better to model a protein superfamily using a single structure-based alignment that is representative of all known cases of the superfamily, or to use multiple sequence-based profiles each representing an individual member of the superfamily. Results: Using profile-profile methods f...
James A. Casbon, Mansoor A. S. Saqi
Added 10 Dec 2010
Updated 10 Dec 2010
Type Journal
Year 2006
Where BMCBI
Authors James A. Casbon, Mansoor A. S. Saqi
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