BASICS OF SEQUENCE ALIGNMENT

1. Click to edit Master title style BASICS OF SEQUENCE ALIGNMENT Submitted by: Anish and Pankaj M.Sc. Systems Biology & Bioinformatics Panjab University, Chandigarh 1

2. Click to edit Master title style INTRODUCTION A sequence alignment is the way of arranging sequences like DNA, RNA and protein to identify similarities like functional, structural evolutionary between sequences • Sequence alignment should be between known and unknown sequence or between two unknown sequences. • Here, known sequence will be called as reference sequence and known sequence will be called query sequence. Types of sequence alignment Local Alignment Global Alignment 2

3. GLOBAL ALIGNMENT Click to edit Master title style • Based on Needleman-Wunsch algorithm • In global alignment, Two sequences to be aligned which are assumed to be similar over entire length. • Where, the alignment is done from beginning to the end of both the sequences to find best possible alignment. Input: Two sequences as potentially equivalent. Goal: To identify the similarity and dissimilarity. 3 3

4. LOCAL ALIGNMENT Click to edit Master title style • Its based on Smith-Waterman algorithm. • Its only find local regions with highest similarity level between two sequences and aligns the regions without assuming that these two sequences have any similarity for entire length. Input: Two sequences may or may not be similar. Goal: Will see substring of one sequence aligns well with the other. 4 4

5. Click to edit Master title style APPLICATIONS Global Alignment Local Alignment • To compare two genes with similar function. • To compare two proteins with similar function. • To search the local similarities in large sequences • To look for the conserved domains or the motifs in two proteins 5 5

6. Click to edit Master title style REFERENCE Xiong, J. (2006). Pairwise Sequence Alignment. In Essential Bioinformatics (pp. 31-50). Cambridge: Cambridge University Press. doi:10.1017/CBO9780511806087.004 6 6