Sequence Analysis Alignments dot-plots scoring scheme Substitution matrices Search algorithms (BLAST)

Slides:

Advertisements

Similar presentations

1 Orthologs: Two genes, each from a different species, that descended from a single common ancestral gene Paralogs: Two or more genes, often thought of.

Advertisements

Sequence Analysis Millions of entries of protein and nucleotide data now in databases - How to convert this to useful information? Sequence analysis -

Sources Page & Holmes Vladimir Likic presentation: 20show.pdf

Measuring the degree of similarity: PAM and blosum Matrix

Global Alignment: Dynamic Progamming Table s 1 : acagagtaac s 2 : acaagtgatc -acaagtgatc - a c a g a g t a a c j s2s2 i s1s1 Scores: match=1, mismatch=-1,

Sequence Similarity Searching Class 4 March 2010.

©CMBI 2005 Sequence Alignment In phylogeny one wants to line up residues that came from a common ancestor. For information transfer one wants to line up.

Sequence alignment SEQ1: VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKK VADALTNAVAHVDDPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHA SLDKFLASVSTVLTSKYR.

Expect value Expect value (E-value) Expected number of hits, of equivalent or better score, found by random chance in a database of the size.

DNA Alignment. Dynamic Programming R. Bellman ~ 1950.

Sequence Analysis Tools

Sequence Comparison Intragenic - self to self. -find internal repeating units. Intergenic -compare two different sequences. Dotplot - visual alignment.

Alignment methods June 26, 2007 Learning objectives- Understand how Global alignment program works. Understand how Local alignment program works.

Bioinformatics Unit 1: Data Bases and Alignments Lecture 3: “Homology” Searches and Sequence Alignments (cont.) The Mechanics of Alignments.

Dynamic Programming. Pairwise Alignment Needleman - Wunsch Global Alignment Smith - Waterman Local Alignment.

Needleman_Wunsch algorithm of global alignment Chap. 6 Higgs and Attwood.

Alignment methods II April 24, 2007 Learning objectives- 1) Understand how Global alignment program works using the longest common subsequence method.

Basics of Sequence Alignment and Weight Matrices and DOT Plot

TGCAAACTCAAACTCTTTTGTTGTTCTTACTGTATCATTGCCCAGAATAT TCTGCCTGTCTTTAGAGGCTAATACATTGATTAGTGAATTCCAATGGGCA GAATCGTGATGCATTAAAGAGATGCTAATATTTTCACTGCTCCTCAATTT.

Presented by Liu Qi Pairwise Sequence Alignment. Presented By Liu Qi Why align sequences? Functional predictions based on identifying homologues. Assumes:

© Wiley Publishing All Rights Reserved.

Inferring function by homology The fact that functionally important aspects of sequences are conserved across evolutionary time allows us to find, by homology.

Brandon Andrews.  Longest Common Subsequences  Global Sequence Alignment  Scoring Alignments  Local Sequence Alignment  Alignment with Gap Penalties.

Pairwise & Multiple sequence alignments

An Introduction to Bioinformatics

. Sequence Alignment and Database Searching 2 Biological Motivation u Inference of Homology  Two genes are homologous if they share a common evolutionary.

Protein Sequence Alignment and Database Searching.

Computational Biology, Part 3 Sequence Alignment Robert F. Murphy Copyright  1996, All rights reserved.

Chapter 11 Assessing Pairwise Sequence Similarity: BLAST and FASTA (Lecture follows chapter pretty closely) This lecture is designed to introduce you to.

Alineamiento Matricial (Harr Plot, Matrix Plot, Dot Plot, Dot Matrix)

BCB 444/544 F07 ISU Dobbs #4 - Sequence Alignment

Sequence Alignment Techniques. In this presentation…… Part 1 – Searching for Sequence Similarity Part 2 – Multiple Sequence Alignment.

Sequence Alignment Goal: line up two or more sequences An alignment of two amino acid sequences: …. Seq1: HKIYHLQSKVPTFVRMLAPEGALNIHEKAWNAYPYCRTVITN-EYMKEDFLIKIETWHKP.

Alignment methods April 26, 2011 Return Quiz 1 today Return homework #4 today. Next homework due Tues, May 3 Learning objectives- Understand the Smith-Waterman.

Pairwise Sequence Alignment BMI/CS 776 Mark Craven January 2002.

Pairwise alignment of DNA/protein sequences I519 Introduction to Bioinformatics, Fall 2012.

Sequence Analysis CSC 487/687 Introduction to computing for Bioinformatics.

Scoring Matrices April 23, 2009 Learning objectives- 1) Last word on Global Alignment 2) Understand how the Smith-Waterman algorithm can be applied to.

Sequence alignment SEQ1: VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKK VADALTNAVAHVDDPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHA SLDKFLASVSTVLTSKYR.

Construction of Substitution Matrices

Sequence Alignment Only things that are homologous should be compared in a phylogenetic analysis Homologous – sharing a common ancestor This is true for.

Basic terms:  Similarity - measurable quantity. Similarity- applied to proteins using concept of conservative substitutions Similarity- applied to proteins.

COT 6930 HPC and Bioinformatics Sequence Alignment Xingquan Zhu Dept. of Computer Science and Engineering.

Applied Bioinformatics Week 3. Theory I Similarity Dot plot.

Sequence Alignments with Indels Evolution produces insertions and deletions (indels) – In addition to substitutions Good example: MHHNALQRRTVWVNAY MHHALQRRTVWVNAY-

341- INTRODUCTION TO BIOINFORMATICS Overview of the Course Material 1.

Pairwise sequence alignment Lecture 02. Overview  Sequence comparison lies at the heart of bioinformatics analysis.  It is the first step towards structural.

Sequence Alignment.

Construction of Substitution matrices

Sequence Alignment Abhishek Niroula Department of Experimental Medical Science Lund University

Step 3: Tools Database Searching

Last lecture summary. identity vs. similarity homology vs. similarity gap penalty affine gap penalty gap penalty high fewer gaps, if investigating related.

Day 7 Carlow Bioinformatics Aligning sequences. What is an alignment? CENTRAL concept in bioinformatics Easy if straight-forward, similar seqs –THISTHESAME.

. Sequence Alignment Author:- Aya Osama Supervision:- Dr.Noha khalifa.

Sequence Alignment. Assignment Read Lesk, Problem: Given two sequences R and S of length n, how many alignments of R and S are possible? If you.

Last lecture summary.

Techniques for Protein Sequence Alignment and Database Searching G P S Raghava Scientist & Head Bioinformatics Centre, Institute of Microbial Technology,

Last lecture summary. Sequence alignment What is sequence alignment Three flavors of sequence alignment Point mutations, indels.

Tutorial 4 Comparing Protein Sequences Intro to Bioinformatics 1.

Sequence Analysis Topics to be covered What is sequence analysis? Why we need it? How we do it? What are the tools available?

Bioinformatics for Research

Bioinformatics: The pair-wise alignment problem

In-Text Art, Ch. 16, p. 316 (1).

#5 - Dynamic Programming

Pairwise Sequence Alignment

Sequence Alignment.

30% grade = class presentations

Pairwise Sequence Alignment

Bioinformatics Lecture 2 By: Dr. Mehdi Mansouri

Sequence Analysis Alan Christoffels

Presentation transcript:

Sequence Analysis Alignments dot-plots scoring scheme Substitution matrices Search algorithms (BLAST)

Why Compare Sequences?

Positions not critical to function can mutate randomly!!!!!

Sequence Comparisons Homology similarity due to a common ancestor no degrees of homology Paralogy Orthology Homework: Define para/ ortholog

Sequence Comparisons

S O U T H A F R I C A S O O T H A F R I C A What is a Sequence Alignment?

S O U T H A F R I C A S O O T H A F R I C A

What is a Sequence Alignment? S O U T H A F R I C A S O O T H A F R I C A S O U T H A F R I C A S O U T H A F R I K A

What is a Sequence Alignment? S O U T H A F R I C A S O O T H A F R I C A S O U T H A F R I C A S O U T H A F R I K A

What is a Sequence Alignment? S O U T H A F R I C A S O O T H A F R I C A S O U T H A F R I C A S O U T H A F R I K A S O U T H A F R I C A S O U T - A F R I C A

What is a Sequence Alignment? S O U T H A F R I C A S O O T H A F R I C A S O U T H A F R I C A S O U T H A F R I K A S O U T H A F R I C A S O U T - A F R I C A gap

S O - T H A F R I C A S O O T H - F R I K A N S - O T H A F R I C A S O O T H - F R I K A N Uncertainty in Alignments

S O U T H A F R I C A S O U T H - - R I K A N substitution gaps Gaps, Insertions, Deletions (Indels) & Substitutions

Global vs. Local Alignment

End-to-end

Global vs. Local Alignment End-to-end Not aligned Homework: Define

Global vs. Local Alignment End-to-end Not aligned Homework: When do you use which?

Dot Plots Dot-plot of a sequence against itself

Homework: What do palindromes look like in a dot-plot? More dot plot examples Internal Repeats Insertion/ Deletion Divergence

Dynamic Programming

Note the Repeats

Dynamic Programming Repeats

Dynamic Programming Repeats

Dynamic Programming Repeats

Which Alignment is Best?

Which Alignment is Best?