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

This preview shows pages 1–2. Sign up to view the full content.

This preview has intentionally blurred sections. Sign up to view the full version.

View Full Document
This is the end of the preview. Sign up to access the rest of the document.

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...
View Full Document

## 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.

### Page1 / 3

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

This preview shows document pages 1 - 2. Sign up to view the full document.

View Full Document
Ask a homework question - tutors are online