On single and multiple models of protein families for the detection of remote sequence relationships |
| |
Authors: | James A Casbon Mansoor AS Saqi |
| |
Institution: | (1) Bioinformatics Group, Institute of Cell and Molecular Science, The Genome Centre, Queen Mary's School of Medicine and Dentistry, Charterhouse Square, London, EC1M 6BQ, UK |
| |
Abstract: | 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. |
| |
Keywords: | |
本文献已被 SpringerLink 等数据库收录! |
|