We consider the problem of multiple sequence alignment: given k sequences of length at most n and a certain scoring function, find an alignment that minimizes the corresponding "sum of pairs" distance score. We generalize the divide-and-conquer technique described in [1,2], and present new ideas on how to use efficient search strategies for saving computer memory and accelerating the procedure ...

UNLABELLED Two methods to add unaligned sequences into an existing multiple sequence alignment have been implemented as the '--add' and '--addfragments' options in the MAFFT package. The former option is a basic one and applicable only to full-length sequences, whereas the latter option is applicable even when the unaligned sequences are short and fragmentary. These methods internally infer the...

Background: Dialign is a DNA/Protein alignment tool for performing pairwise and multiple pairwise alignments through the comparison of gap-free segments (fragments) between sequence pairs. An alignment of two sequences is a chain of fragments, i.e local gap-free pairwise alignments, with the highest total score. METHOD: A new approach is defined in this article which relies on the concept of us...

Recently, there has been a growing interest in the use of mosaic images to represent the information contained in video sequences. This paper systematically investigates how to go beyond thinking of the mosaic simply as a visualization device, but rather as a basis for an eecient and complete representation of video sequences. We describe two diierent types of mosaics called the static and the ...

MOTIVATION Membrane proteins are clinically relevant, yet their crystal structures are rare. Models of membrane proteins are typically built from template structures with low sequence identity to the target sequence, using a sequence-structure alignment as a blueprint. This alignment is usually made with programs designed for use on soluble proteins. Biological membranes have layers of varying ...

A large number of methods for multiple sequence alignment are currently available. Recent benchmarking tests demonstrated that strengths and drawbacks of these methods differ substantially. Global strategies can be outperformed by approaches based on local similarities and vice versa, depending on the characteristics of the input sequences. In recent years, mixed approaches that include both gl...

This chapter is a brief introduction to two important statistical methods— maximum likelihood estimation and hypothesis testing. We shall show how to use these methods to test the biological sequence models developed in previous chapters against experimental data. We shall also show how hypothesis testing ideas inspire scoring methods for sequence alignment. denote the outcome of an experiment ...

MOTIVATION The Alvira tool is a general purpose multiple sequence alignment viewer with a special emphasis on the comparative analysis of viral genomes. This new tool has been devised specifically to address the problem of the simultaneous analysis of a large number of viral strains. The multiple alignment is embedded in a graph that can be explored at different levels of resolution. AVAILABI...

During the last years several new tools applicable to protein analysis have made available on the IBIVU web site. Recently, a number of tools, ranging from multiple sequence alignment construction to domain prediction, have been updated and/or extended with services for programmatic access using SOAP. We provide an overview of these tools and their application.

We introduce PASTA, a new method for multiple sequence alignment of datasets with up to 200,000 sequences in [3]. Here we provide supplementary information not provided in the main paper. We give exact commands used for running the experiments, we provide extra results that did not fit in the main paper, and we provide some supplementary discussion of the results.