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Multiple sequence alignment (MSA) is the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. These alignments are used to infer evolutionary relationships via phylogenetic analysis and can highlight homologous features between sequences.
Multiple sequence alignment is an extension of pairwise alignment to incorporate more than two sequences at a time. Multiple alignment methods try to align all of the sequences in a given query set. Multiple alignments are often used in identifying conserved sequence regions across a group of sequences hypothesized to be evolutionarily related.
The rest of this article is focused on only multiple global alignments of homologous proteins. The first two are a natural consequence of most representations of alignments and their annotation being human-unreadable and best portrayed in the familiar sequence row and alignment column format, of which examples are widespread in the literature.
Software to align DNA, RNA, protein, or DNA + protein sequences via pairwise and multiple sequence alignment algorithms including MUSCLE, Mauve, MAFFT, Clustal Omega, Jotun Hein, Wilbur-Lipman, Martinez Needleman-Wunsch, Lipman-Pearson and Dotplot analysis. Both: Both: DNASTAR: 1993-2016 MUMmer suffix tree based: Nucleotide: Global: S. Kurtz et ...
The frame used was frame 1 for the DNA sequence. As shown in the picture, there was a gap of 2 amino acids (6 nucleic acids) in the alignment, which results the total low score of -2. Figure 2 illustrates the aligned result using PairWise. Using the same DNA and protein sequence, and with the penalties modified as below.
The multiple sequence alignment problem is generally based on pairwise sequence alignment and currently, for a pairwise sequence alignment problem, biologists can use a dynamic programming approach to obtain its optimal solution. However, the multiple sequence alignment problem is still one of the more challenging problems in bioinformatics.
Clustal Omega has five main steps in order to generate the multiple sequence alignment. A pairwise alignment is produced using the k-tuple method.This is a heuristic method that isn't guaranteed to find an optimal solution, but is more efficient than using dynamic programming. Sequences are clustered using the modified mBed method. [22]
Distance-matrix methods of phylogenetic analysis explicitly rely on a measure of "genetic distance" between the sequences being classified, and therefore they start with a multiple sequence alignment (MSA) as an input. From it, they construct an all-to-all matrix describing the distance between each sequence pair.