Focus of this presentation Meaning of Sequence Alignment Global and Local Alignment of Sequences Pairwise and Multiple Sequence Alignment Scoring of Aligned Sequences Significance of Sequence Alignment Sequence Alignment Programs Tutorials Sequence Alignment • Sequence alignment is the procedure of comparing two (pair-wise alignment) or more (multiple sequence alignment) sequences by searching for a series of individual characters or character patterns that are in the same order in the sequences. • Probably the most common experiment done in modern day ...
CONTENTS 1. Sequence Alignment - Why align sequences 2. Sequence Alignment Methods - Pairwise Alignment - Multiple Sequence Alignment 3. Pairwise Sequence Alignment Methods -Global Alignment (Needleman- Wunsch) - Local Alignment (Smith-Waterman) 1. Sequence Alignment Why and how align sequences Sequence Alignment A way of arranging the sequences of DNA, RNA, or protein to identify CTGTCG-CTGCACG regions of similarity that may be a consequence of functional, -TGC-CG-TG---- structural, or evolutionary relationships between the sequences Why align sequences? • Useful for ...
Multiple sequence alignments Multiple Sequence Alignment (MSA) can be seen as a generalization of a Pairwise Sequence Alignment (PSA). Instead of aligning just two sequences, three or more sequences are aligned simultaneously. MSA is used for: • Detection of conserved domains in a group of genes or proteins • Construction of a phylogenetic tree • Prediction of a protein structure (e.g., AlphaFold, RoseTTAFold) • Determination of a consensus sequence (e.g., transposons) Multiple sequence alignments Example: part of an ...
Multiple Alignment Stuart M. Brown NYU School of Medicine Learning Objectives Understand the need for multiple alignment methods in biology Optimal methods (dynamic programming) are not practical to align many sequences Progressive pairwise approach Profile alignments Editing alignments Sequence Logos Reasons for aligning sets of sequences Organize data to reflect sequence homology Estimate evolutionary distance Infer phylogenetic trees from homologous sites Highlight conserved sites/regions (motifs) Highlight variable sites/regions Uncover changes in gene structure Look for evidence of selection Summarize information ...
Finds seeds and extend: Blast HEURISTICS FOR EFFICIENT COMPUTATION OF NEAR-OPTIMAL ALIGNMENTS 08/28/2022 2 Alignment method needs to fit the problem, part 1 Problem Features Method Example of program Pairwise alignment of Moderate size Dynamic Needleman-Wunsch proteins or genes (hundreds of letters), programming, find (needle in similar throughout optimal global EMBOSS/Galaxy) alignment Moderate size Dynamic Smith-Waterman (hundreds of letters), programming, find (water in subsequences similar optimal local EMBOSS/Galaxy) alignment Find a match between Query sequence could Heuristic approach; Blast family ...
PWA vs MSA • Pairwise sequence alignment (PWA) is much faster and has very high correlation with multiple sequence alignment (MSA). 1.2 MSA SWG NW 1 n0.8 o i t a0.6 l e r r o0.4 C 0.2 0 599nts 454 optimized 999nts The comparison using Mantel between distances generated by three sequence alignment methods and RAxML Summarize a million Fungi Sequences Spherical Phylogram Visualization RAxML result visualized in FigTree. Spherical Phylogram visualized in PlotViz ...
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