1. What is Alignment ? One of the oldest techniques used in computational biology The goal of alignment is to establish the degree of similarity between two sequences in order to establish the degree of similarity and the possibility of homology (similarity due to shared ancestry) The results from alignments can be used to make hypotheses regarding the function and relatedness of biological sequences Sequence alignment serves as the basis for searching biological data

2. How Does Alignment Work? Each pairwise alignment is assigned a score based on the quality of the match –If the pairs are identical, it is considered a match –A position where a letter is matched with a null is called a gap or indel (insertion/deletion) –A position where the pairs are different is called a mismatch The scores assigned to each alignment can be altered in order to tailor the results Each possible alignment of the two sequences is scored and the one with the best overall score is selected

3. SIMPLE ALIGNMENT Below are four possible alignments of the sequences “AT” and “A” Every possible combination of “A” and “AT” can be scored Consider the sequences “ATGAGAC” and “CTAGAC” Assume a score of +1 where a match occurs, a -1 for a mismatch, and 0 for a gap The table to the right displays possible alignments and their respective scores The highest scoring alignment is the one selected ALIGNMENTSCORE A T G A G A C | | | | | | | C T A G A C - -5 + 1 = -4 A T G A G A C | | | | | | | C T - A G A C -1 + 5 = 4 A T G A G A C | | | | | | | - C T A G A C -2 + 4 = 2 - A T G A G A C | | | | C - T - A G A C -0 + 5 = 5 1)A T 2)A T| | A ---- A 3)A T -- 4) -- A T | | | -- -- A A -- --

4. TYPES OF ALIGNMENT Sequence alignments are either –Global Finds best match over total length of both sequences More useful amongst closely related sequences Less commonly used –Local Finds best matching segments between two sequences More flexible technique, therefore widely used –Fit (Semi-global) Fits entire structural domain into the sequence S1 S2 GLOBAL ALIGNMENT S1 S2 LOCAL ALIGNMENT S1 S2 GLOBAL LOCAL FIT ALIGNMENT