One of the most fundamental operations in biological sequence analysis is multiple sequence alignment (MSA). It is a critical tool for biologists to identify the relationships between species and also possibly predict the structure and functionality of biological sequences. The general multiple sequence alignment problem is known to be NP-hard, and hence the problem of finding the best possible...

Proteins or genes that have similar sequences are likely to perform the same function. One of the most widely used techniques for sequence comparison is sequence alignment. Sequence alignment allows mismatches and insertion/deletion, which represents biological mutations. Sequence alignment is usually performed only on two sequences. Multiple sequence alignment, is a natural extension of two-se...

BIOLOGICALLY RELEVANT MULTIPLE SEQUENCE ALIGNMENT Hyrum D. Carroll Department of Computer Science Doctor of Philosophy Researchers use multiple sequence alignment algorithms to detect conserved regions in genetic sequences and to identify drug docking sites for drug development. In this dissertation, a novel algorithm is presented for using physicochemical properties to increase the accuracy of...

Multiple protein sequence alignment is an extension of pairwise alignment to incorporate more than two sequences at a time. Multiple protein sequence alignment methods try to align all of the sequences in a given query set. Multiple protein sequence alignments are often used in identifying conserved sequence regions across a group of sequences hypothesized to be evolutionarily related. Many app...

Our analyses of ultra-conserved elements are based on multiple sequence alignments produced by MAVID [Bray and Pachter, 2004]. Prior to the alignment of multiple genomes, homology mappings (from Mercator [Dewey, 2005]) group into bins genomic regions that are anchored together by neighboring homologous exons. A multiple sequence alignment is then produced for each of these alignment bins. MAVID...

Figure 1: The art of multiple sequence alignment. This document is intended to illustrate the art of multiple sequence alignment in R using DECIPHER. Even though its beauty is often concealed, multiple sequence alignment is a form of art in more ways than one. Take a look at Figure 1 for an illustration of what is happening behind the scenes during multiple sequence alignment. The practice of s...

Multiple DNA sequence alignment is an important research topic of bioinformatics. In this paper, we present a new method for multiple DNA sequence alignment, based on genetic simulated annealing techniques, to choose the best cutting point set of the multiple DNA sequence set. The experimental results show that the proposed method gets higher scores and more match columns than the method presen...

SUMMARY Improving and ascertaining the quality of a multiple sequence alignment is a very challenging step in protein sequence analysis. This is particularly the case when dealing with sequences in the 'twilight zone', i.e. sharing < 30% identity. Here we describe INTERALIGN, a dedicated user-friendly alignment editor including a view of secondary structures and a synchronized display of carbon...

Obtaining high quality multiple alignments is crucial for a range of sequence analysis tasks. A common strategy is to align the sequences several times, varying the program or parameters until the best alignment according to manual inspection by human experts is found. Ideally, this should be assisted by an automatic assessment of the alignment quality. Our web-site http://msa.cgb.ki.se allows ...