# Algorithms in Bioinformatics FOUR Pairwise Sequence Alignment. Pairwise Sequence Alignment. Convention: DNA Sequences 5. Sequence Alignment

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1 Algorithms in Bioinformatics FOUR Sami Khuri Department of Computer Science San José State University Pairwise Sequence Alignment Homology Similarity Global string alignment Local string alignment Dot matrices Dynamic programming Scoring matrices BLAST Convention: DNA Sequences 5 3 A T C G A T G C T A A T C G C G A T G C A T 5 ACAGTACCAGACCAGACCATACATACCATC 3 3 TGTCATGGTCTGGTCTGGTATGTATGGTAG 5 ACAGTACCAGACCAGACCATACATACCATC 3 5 Sequence Alignment Sequence alignment is the procedure of comparing sequences by searching for a series of individual characters or character patterns that are in the same order in the sequences. Comparing two sequences gives us a pairwise sequence alignment. Comparing more than two sequences gives us multiple sequence alignment. Pairwise vs Multiple Alignment Infer biological relationships from the sequence similarity Multiple Sequence Alignment Infer sequence similarity from biological relationships Starting point: sequences that are biologically related. Use the MSA to infer phylogenetic relationships. They can help elucidate biological facts about proteins since most conserved regions are biologically significant. MSA s can help formulate and test hypotheses about protein 3-D structure and function. Why Do We Align Sequences? Phylogenetic trees and molecular evolution Identifying genes in a genome Predicting function of unknown genes Predicting protein structure Assembling genome sequences 4.1

2 Why Do We Align Sequences? The basic idea of aligning sequences is that similar DNA sequences generally produce similar proteins. To be able to predict the characteristics of a protein using only its sequence data, the structure or function information of known proteins with similar sequences can be used. To be able to check and see whether two (or more) genes or proteins are evolutionarily related to each other. Importance of Alignments Alignment methods are at the core of many of the software tools used to search the databases. Alignment is the task of locating equivalent regions of two or more sequences to maximize their similarity. In order to assess the similarity of two sequences it is necessary to have a quantitative measure of their alignment, which includes the degree of similarity of two aligned residues as well as accounting for insertions and deletions. Query Sequence If a query sequence is found to be significantly similar to an already annotated sequence (DNA or protein), we can use the information from the annotated sequence to possibly infer gene structure or function of the query sequence. Similarity and Difference The similarity of two DNA sequences taken from different organisms can be explained by the theory that all contemporary genetic material has one common ancestral DNA. Differences between families of contemporary species resulted from mutations during the course of evolution. Most of these changes are due to local mutations between nucleotide sequences. When To Do The Pairwise Comparison? You have a strong suspicion that two sequences are homologous. Two sequences are homologous, when they share a common ancestor. Homology and Similarity Homology Evolutionary related sequence. A common ancestral molecular sequence. Similarity Sequences that share certain sequence patterns. Directly observable from alignment. 4.2

3 Homology Common ancestry Sequence (and usually structure) conservation Homology is not a measurable quantity Homology can be inferred, under suitable conditions. Similarity Most common method for comparing sequences. Similarity is a measurable quantity The degree of similarity depends on the parameters used (alphabet, scoring matrix, etc.). Identity Most objective measuring entity for comparing sequences. Identity is well-defined. Identity can be quantified as the percentage of identical characters. In other words: The number of identical matches divided by the length of the aligned region. Evolution and Alignments Alignments reflect the probable evolutionary history of two sequences. Residues that align and that are not identical represent substitutions. Sequences without correspondence in aligned sequences are interpreted as indels and in an alignment are gaps. How do we Compare Sequences? Substitution Read from top to bottom: Deletion Read from bottom to top: Insertion Determining the similarity of two genes by aligning their nucleotide sequences as well as possible; the differences due to mutation are shown in boxes. Quantifying Alignments The alignment score can be used to estimate the biological difference of two DNA or protein sequences. How should alignments be scored? Do we use +1 for a match and -1 for a mismatch? Should we allow gaps to open the sequence so as to produce better matches elsewhere in the sequence? If gaps are allowed, how should they be scored? 4.3

4 Need for Gaps: An Example Without gaps: Only 4 matches between the 2 sequences With gaps: 11 matches between the 2 sequences Scoring a Pairwise Alignment The two sequences are 70% identical mismatch (substitution) Indel (insertion deletion) A C C T G A G A G A C G T G G C A G Score of the alignment where: Match à +1 Mismatch à -1 Indel à -2 score of alignment 1 +1+(-1)+1+1+(-2)+1+(-2)+1 +1 = +2 Problem Definition Local and Global Alignments Given: Two sequences. A scoring system for evaluating match or mismatch of two characters. A penalty function for gaps in sequences. Find: An optimal pairing of sequences that retains the order of characters in each sequence, perhaps introducing gaps, such that the total score is optimal. Global alignment find alignment in which the total score is highest, perhaps at the expense of areas of great local similarity. Local alignment find alignment in which the highest scoring subsequences are identified, at the expense of the overall score. Local alignment can be obtained by performing minor modifications to the global alignment algorithm. Shall we perform: Global or Local Alignment? Global Alignment: Are these two sequences generally the same? Local Alignment: Do these two sequences contain high scoring subsequences? Local similarities may occur in sequences with different structure or function that share common substructure or subfunction. Local Sequence Alignment The optimal local alignment of two sequences is the one that finds the longest segment of high sequence similarity between the two sequences. 4.4

5 Example: Local and Global Alignments Local alignment Global alignment Methods of Alignment A) By hand - slide sequences on two lines of a word processor B) Dot plot (also known as dot matrix) with windows C) Rigorous mathematical approach Dynamic programming (optimal but slow) D) Heuristic methods (fast but approximate) BLAST and FASTA Word matching and hash tables A) Pairwise Sequence Alignment by Hand Write sequences across the page in two rows. Place identical or similar characters in the same column. Place non-identical characters either in the same column as a mismatch or opposite a gap in the other sequence. B) Dot Matrix Method (I) Dot matrices are the simplest means of comparing two sequences. Dot matrices are designed to answer the following questions: Where are all sites of similarity between my sequence and a second sequence? Where are all sites of internal similarity in my sequence? Dot plots are not quantitative, they are qualitative. The Dot Matrix Method (II) Dot plots place one sequence on the X axis, the other on the Y axis and compare the sequence on one axis with that on the other: If the sequences match according to some criteria, a dot is placed at the XY intercept. The dots populate a 2-dimentional space representing similarity between the sequences along the X and the Y axes. Dot plots present a visual representation of the similarity between two sequences, but do not give a numerical value to this similarity. A T G C C T A G Dot Matrices A T G C C T A G Window Size = 1 The diagonal line always appears when a sequence is compared to itself. 4.5

6 Background Noise Red dots represent identities that are meaningful they are true matchings of identical residue-pairs. Pink dots represent identities that are due to noise they are matchings of random identical residues-pairs Improving Dot Matrices In a dot matrix, detection of matching regions may be improved by filtering out random matches. Filtering is achieved by using a sliding window to compare the two sequences. Sliding Window Dot Matrices with Windows 4 GAA CTCA TACGAATTCACATTAGAC Window Size: Number of characters to compare Stringency: Number of characters that have to match exactly There are some default values for the window size and for the stringency, but one has to play around with the numbers to see what gives the best result. A T G C C T A G A T G C C T A G Window Size = 2 Compare two nucleotides at a time. Windows filter out the noise. Internal Repeats Determining Window Size DNA Sequences A typical window size is15. A suitable match (stringency) requirement in this window is 10. Protein Sequence Often the matrix is not filtered, but a window size requirement is 2 or 3. A match requirement of 2 will highlight matching regions. 4.6

7 Advantages of Dot Matrix All possible matches of residues between two sequences are found The investigator now has the choice of identifying the most significant ones. The sequences of the actual regions that align can be detected by using one of two other methods for performing sequence alignments. The presence of insertions/deletions and direct and inverted repeats can be revealed. Dot Matrices Shortcomings Most dot matrix computer programs do not show an actual alignment. Dot matrices rely on visual analysis. It is difficult to find optimal alignments. We need scoring schemes more sophisticated than identical match. It is difficult to estimate the significance of alignments. Dot matrices do not allow gaps in the sequence alignments. Other Applications of Dot Matrix Finding direct, inverted or tandem repeats in protein and DNA sequences. Predicting regions in RNA that are selfcomplementary and that have the potential of forming secondary structure. C) Dynamic Programming Dynamic programming provides a reliable and optimal computational method for aligning DNA and protein sequences. The optimal alignments provide useful information to researchers, who make functional, structural, and evolutionary predictions of the sequences. Needleman Wunsch: Example Find the optimal alignment between: TCCA and TCGCA Scoring Function: +1 for match -1 for mismatch -2 for gap Solution: T C - C A : : : : T C G C A = 2 Local Sequence Alignment Their dynamic algorithm gives a global alignment of sequences. A modification of the dynamic programming algorithm for sequence alignment provides a local sequence alignment giving the highestscoring local match between two sequences (Smith and Waterman 1981). Local alignments are usually more meaningful than global matches because they include patterns that are conserved in the sequences. 4.7

8 Local Alignments Scoring Systems G A A C G T A G G C G T A T A T A C T A C G G A G G G Thus, the best local alignment achieved from the above Dynamic Programming is: A C G G A G G A C G T A G G Use of the dynamic programming method requires a scoring system for the comparison of symbol pairs (nucleotides for DNA sequences & amino acids for protein sequences), a scheme for insertion/deletion (gap) penalties. The most commonly used scoring systems for protein sequence alignments are the log odds form of the PAM250 matrix and the BLOSUM62 matrix. A number of other choices are available. Successful Substitution Matrices The most successful substitution matrices are the ones that use actual evidence of what has happened during evolution, and are based on the analysis of alignments of numerous homologs of well-suited proteins from many different species. Scoring Matrices (I) Upon evaluating a sequence alignment, we are really interested in knowing whether the alignment is random or meaningful. A scoring matrix (table) or a substitute matrix (table) is a table of values that describe the probability of a residue (amino acid or base) pair occurring in an alignment. Scoring Matrices II The alignment algorithm needs to know if it is more likely that a given amino acid pair has occurred randomly or that it has occurred as a result of an evolutionary event. Similar amino acids are defined by highscoring matches between the amino acid pairs in the substitution matrix. Amino Acid Substitution Matrices (I) For proteins, an amino acid substitution matrix, such as the Dayhoff Percent Accepted Mutation matrix 250 (PAM250) or Block Substitution Matrix 62 (BLOSUM62) is used to score matches and mismatches. Similar matrices are available for aligning DNA sequences. 4.8

9 Amino Acid Substitution Matrices (II) In the amino acid substitution matrices, amino acids are listed both across the top of a matrix and down the side, and each matrix position is filled with a score that reflects how often one amino acid would have been paired with the other in an alignment of related protein sequences. PAM Matrices Point Accepted Mutation An accepted mutation is any mutation that doesn t kill the protein or organism; that is, amino acid changes accepted by natural selection. One PAM (PAM1) = 1% of the amino acids have been changed. Dayhoff Amino Acid Substitution Matrices PAM Matrices are Dayhoff amino acid substitution or percent accepted mutation matrices. This family of matrices lists the likelihood of change from one amino acid to another in homologous protein sequences during evolution. These predicted changes are used to produce optimal alignments between two protein sequences and to score the alignment. Extrapolating PAM1 The assumption in this evolutionary model is that the amino acid substitutions observed over short periods of evolutionary history can be extrapolated to longer distances. Constructing More PAM Matrices The PAM1 Matrix is best used for comparing sequences where 1% or less of the amino acids have changed. What do you do with sequences that are more divergent? You multiply the PAM1 matrix by itself N times to get a new matrix that works best with sequences that have PAM2, PAM20, PAM100, PAM200, etc. For example PAM20 = (PAM1) 20 PAM Matrices for Low Level of Similarities As seen, PAM1 matrix could be multiplied by itself N times, to give transition matrices for comparing sequences with lower and lower levels of similarity due to separation of longer periods of evolutionary history. The PAM120, PAM80, and PAM60 matrices should be used for aligning sequences that are 40%, 50%, and 60% similar, respectively. 4.9

10 PAM250 Matrix BLOSUM vs PAM The PAM250 matrix provides a betterscoring alignment than lower-numbered PAM matrices for distantly related proteins of 14-27% similarity. Scoring matrices are also used in database searches for similar sequences. The BLOSUM matrix was constructed from actual substitutions. The BLOSUM matrix was derived much more recently than the Dayhoff matrices, in the early 1990 s, using local multiple alignments rather than global alignments. BLOSUM Matrices The BLOSUM scoring matrices (especially BLOSUM62) appear to capture more of the distant types of variations found in protein families. Another criticism: PAM scoring matrices are not much more useful for sequence alignment than simpler matrices, such as the ones based on chemical grouping of amino acid side chains. BLOSUM Block Substitution Matrix created from BLOCKS database. Currently the most widely used comparison matrix. More sensitive than PAM or other matrices Finds more sequences that are related The BLOSUM matrices are based on an entirely different type of sequence analysis and a much larger data set than the Dayhoff PAM Matrices. BLOSUM62 Substitution Matrix Small and polar PAM120 Substitution Matrix Small and nonpolar Polar or acidic Basic Large and hydrophobic Aromatic Colors indicate different physicochemical properties of the residues. 4.10

11 Comparison: PAM and BLOSUM Matrices The PAM model is designed to track the evolutionary origins of proteins, whereas the BLOSUM model is designed to find their conserved domains. D) Approximate Methods BLAST Basic Local Alignment Search Tool Altschul et al. 1990,1994,1997 Heuristic method for local alignment Designed specifically for database searches Idea: Good alignments contain short lengths of exact matches. The BLAST Family blastp: compares an amino acid query sequence against a protein sequence database. blastn: compares a nucleotide query sequence against a nucleotide sequence database. blastx: compares the six-frame conceptual translation products of a nucleotide query sequence (both strands) against a protein sequence database. Chance or Homology? In all methods of sequence comparison, the fundamental question is whether the similarities perceived between two sequences are due to chance, and are thus of little biological significance, or whether they are due to the derivation of the sequences from a common ancestral sequence, and are thus homologous. The Expected Value Blastn: general purpose nucleotide search and alignment program to align trna or rrna sequences as well as mrna or genomic DNA sequences containing a mix of coding and noncoding regions. The e-value tells us how likely it is that the similarity between the query sequence and the database sequence is due to chance. The lower the e-value, the more likely it is that the two sequences are truly similar and not just chance matches 4.11

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