If more than two sequences are mutually similar above the current cutoff score, then all are brought together in one step using a fast concatenation algorithm (see ref. On each cycle, only sequences that have a pairwise similarity greater than a predefined cutoff (specified of each cycle) are aligned. Where CLUSTAL takes a more rigorous phylogenetic approach to ordering of sequences prior to alignment, MULTAL uses a simple single-linked clustering iterated over several cycles. Those who wish to use the program only as an alignment/editor for a small number of sequences would be best to seek out the program CAMELON (which is an implementation of MULTAL by Oxford Molecular) or CLUSTAL (see Subheading 3.). These applications are the main topic considered in this section. 143: Protein Structure Prediction: Methods and Protocols Edited by: D.
Outline of the Algorithm The Program MULTAL was originally devised to deal with large numbers of protein sequences that are typically encountered in the analysis of large families (such as the immunogobulins or globins) or in sifting out the often extensive collections of sequences produced as the result of a search across the From: Methods in Molecular Biology, vol. Both are based on the simple heuristic that it is best to align the most similar sequences first and gradually combine these, in a hierarchic manner, into a multiple sequence alignment. In this chapter, we describe two methods that can be used to produce multiple sequence alignments. In the former case, the addition of further sequences can reveal portions of the protein that are important in structure and function (even if that structure or function is unknown), whereas in the latter, the revelation of conserved patterns can help add confidence in the alignment. Both these situations can be helped if the analysis is extended to incorporate more sequences. This ideal transfer of information is, unfortunately, not always attained and can fail either because the two sequences are equally uncharacterized (although they might align quite well) or because the alignment is too poor to be trusted. Where one sequence is of unknown structure and function, its alignment with another sequence that is well characterized in both structure and function immediately reveals the structure and function of the first sequence. Introduction The alignment of protein sequences is the most powerful computational tool available to the molecular biologist. Protein Structure Prediction Methods and Protocols Edited byġ Multiple Sequence Alignment Desmond G.
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