Introduction

MultiSeq (shown in Fig. 1) is a unified bioinformatics analysis environment that allows one to organize, display, and analyze both sequence and structure data for proteins and nucleic acids. MultiSeq was created to allow biomedical researchers to study the evolutionary changes in sequence and structure of proteins across all three domains of life, from bacteria to humans. The comparative sequence and structure metrics as well as analysis tools introduced in the

Figure 1: MultiSeq In VMD

article by O'Donoghue and Luthey-Schulten ¹are part of MultiSeq. In particular, the Luthey-Schulten group has included a structure-based measure of homology $Q_H$ (see 10.2), which takes the effect of insertions and deletions into account and has been shown to produce accurate structure-based phylogenetic trees. Multiple Alignment is an invaluable tool for relating protein structure to its function or misfunction. Therefore, the STAMP structural alignment algorithm, kindly provided by our colleagues Russell and Barton, is included ².

For publication of scientific results based completely or in part on the use of MultiSeq, please reference:

Elijah Roberts, John Eargle, Dan Wright, and Zaida Luthey-Schulten. ``MultiSeq: Unifying sequence and structure data for evolutionary analysis.'' BMC Bioinformatics, 2006, 7:382.