Multiple Sequence Alignment Definition

Multiple sequence alignment is defined as an extension of pair wise sequence alignment to incorporate (unite together) more than two sequences at a time. Multiple alignment methods try to align all of the sequence in a given query set. Multiple alignments are often used is identifying conserved sequence regions across a group of sequences. Multiple alignments can also be used to find out evolutionary details.

Aim of multiple sequence alignment

• Multiple sequence alignment is mainly used to find out the similarity between sequences of a gene family.
• Sometimes multiple sequence alignments can also be used to express the dissimilarity between a set of sequences.
• In most cases the multiple sequence alignment can accurately find out biological data.




A multiple sequence alignment is a 2 dimensional (2D) table, in which rows represent individual sequences and columns represent the residue positions. The database of multiple alignments has a great importance. The power of multiple sequence analysis lies in the ability to find out related sequences from various species and to express the degree of similarity between them. The time taken to compute an alignment; increases exponentially with the number of sequences to be aligned.

Simultaneous alignment methods and progressive alignment methods are the two common procedures in multiple sequence alignments. In simultaneous alignment, all sequences are aligned with in a set at once are very time consuming. The progressive multiple alignment methods align sequences in pairs following the branching order of a family tree.

The most similar are aligned first and more distantly related sequences are added later. By exploiting likely evolutionary relationships, progressive multiple alignment methods are less time consuming.


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