14] Consensus methods for DNA and protein sequence alignment

Abstract

This chapter presents some of the tools that can be used to analyze consensus methods for DNA and protein sequence alignment. Sequence alignment is a popular approach to pattern analysis. Computer alignments are often based on an explicit optimization function, rewarding matches and penalizing mismatches, insertions, and deletions. Sequence alignment often gives useful information about evolutionary or functional relationships between sequences. While dynamic programming methods are very widespread in sequence analysis, there are severe restrictions in computation time with the extension of the dynamic programming methods to allow more than two sequences. A great many biological problems do involve more than two sequences. A very useful feature of our program is that once a consensus word has been identified, the sequences can be realigned on that word and the new alignment reevaluated for additional conserved features. The majority of the amino acids in the sequences has been identified as part of conserved words and has been brought into alignment.