NAME: Geoff Barton

AFFILIATION: University of Dundee, UK

CONTACT: geoff@compbio.dundee.ac.uk

TITLE: "Sequence alignment for molecular replacement"

ABSTRACT: Given the sequence of a protein you are trying to solve the structure of (the query), the first step in molecular replacement is to identify a homologue of known structure (the target). The second step is to obtain an accurate alignment of the query and target sequences. While the final step is to build one or more models of the query based on the target structure. Each step in this process is important, but getting an accurate alignment of query to target is critical to the quality of the search model. In this lecture I will outline some of the ways in which you can obtain good sequence alignments, how you can spot possible problems, and how you can be misled. As part of this, I will also review some of the current programs for sequence alignment and highlight their strengths and weaknesses.