msa - Multiple Sequence Alignment: A Brief Introduction...

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Unformatted text preview: Multiple Sequence Alignment: A Brief Introduction Anoop Sarkar for CMPT-825: Natural Language Processing This is a brief summary of some of the issues in multiple sequence alignment (or in other words, computing the minimum edit distance between multiple strings). The description a summary taken from the references listed at the end of this document. 1 Definitions The multiple sequence alignment (MSA) problem is a more general form of the standard alignment problem between a pair of strings. Let S 1 ,. .. ,S k be the input set of strings (sequences) as assume that K is at least 2. The minimum edit distance is defined as d ( S 1 ,. .. ,S K ) Let be the alphabet. We assume that the underscore character is not part of the alphabet so that we can represent alignments based on inser- tions/deletions in the original string. A multiple sequence alignment A is defined as a two-dimensional character array over the alphabet , where = { } . Given an input set of strings S 1 ,. .. ,S k , the alignment array A has K rows and each row A i is the alignment for string S i . Each MSA induces a pairwise alignment A i,j on the pair of sequences S i , S j . Example: Let S 1 = charge , S 2 = barge and S 3 = sarge . Then the MSA is represented as the alignment array A shown below with the minimum edit distance d ( S 1 ,. .. ,S K ): c h a r g e _ b a r g e _ s a r g e 2 Simple Algorithm The obvious method for computing the alignment array...
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This note was uploaded on 10/01/2009 for the course CS BCB/Co taught by Professor Olivereulenstein during the Fall '06 term at Iowa State.

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msa - Multiple Sequence Alignment: A Brief Introduction...

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