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Dynamic programming and pairwise sequence alignment
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- 2. Introduction Algorithm used indynamic programing • Needleman-Wunsch algorithm • Smith- Waterman algorithm Pairwise sequence alignment • BLASTn • BLASTp Applications of pairwise sequence alignment References 1 November 2019 2
- 3. Dynamic programmingis a computational method that is used to align two proteins or nucleic acids sequences. This method is very important for sequence analysis because it provides the very best or optimal alignment between sequences. Alignment includes matched, mismatched characters and gaps in the two sequences that positioned so that the number of matches between identical or related character is maximum as possible. INTRODUCTION 1 November 2019 3
- 4. Needleman-wunsch Algorithm Developed bySaul.b. needleman & christian.d. wunsch Referred as global alignment Used in aligning 2 closely related sequence Compares the whole sequence Tools:- EMBOSS-Needle, Specialised BLAST Smith-Waterman algorithm Developed by Temple.F.Smith & Michael. S. Waterman Referred as local alignment Used in aligning divergent sequences Compares a patch from the sequence Tools:-EMBOSS-Water, LALIGN 1 November 2019 4
- 5. Fig 1:- Comparisonof Global and Local alignment in general 1 November 2019 5
- 6. Needleman-Wunsch algorithm • Alignsprotein or nucleic acid sequences • Divides a large problem into a series of smaller problems • Uses the solution of smaller problem to reconstruct a solution to the larger problems 1 November 2019 6
- 7. Constructing the matrix Wewill have 2 matrices of 2D representation viz, 1. The score matrix 2. Traceback matrix The N-W algorithm consists of 4 steps:- 1. Initialization of the score matrix 2. Filling up the matrix 3. Traceback 4. Alignment 1 November 2019 7
- 8. 1.Initializing the scoringmatrix G C A T G C 0 -1 -2 -3 -4 -5 -6 G -1 T -2 A -3 C -4 G -5 C -6 Match = 1 Mismatch. = -1 Gap. = -1 1 November 2019 8
- 9. 2. Filling thematrix G 0 -1 G -1 X For x : This cell has 3 possible values • Top :- (-1)+(-1) = -2 • Left :- (-1)+(-1) = -2 • Top-left :- (0)+(1) = 1 The highest value is 1 and thus it is entered into the cell i.e x = 1 G 0 -1 G -1 1 1 November 2019 9
- 10. Contd.. G C 0 -1-2 G -1 1 X C -2 Y For X : Top: (-2)+(-1) = (-3) Left: (+1)+(-1) = (0) Top-Left: (-1)+(-1) = (-2) For Y : Top: (1)+(-1) = (0) Left: (-2)+(-1) = (-3) Top-Left: (-1)+(-1) = (-2) The highest value for X and Y is 0, thus it is entered into the cell. i.e X = O; Y = 0 G C 0 -1 -2 G -1 1 0 C -2 0 1 November 2019 10
- 11. 3. Traceback 1 November2019 11
- 12. 4. Alignment Rules :- 1.If arrow is vertical/horizontal assign a gap and a character :- Gaps and characters Where to Assign a gap and a character ? Sequence 1 or 2 1 November 2019 12
- 13. Contd… Ans) The gapwill be assigned in the direction of the arrow and the character will be assigned in the opposite direction 2. If there is a diagonal arrow both the characters will be assigned :- Both characters 1 November 2019 13
- 14. Result of alignment GC T A G C - . . G - T A C G C 1 November 2019 14
- 15. • S-W algorithmis modified version of Needleman- Wunsch algorithm • Negative scoring matrix cells are set to zero • Traceback procedure starts at the highest scoring matrix cells and procedure until a cell with score zero is found 1 November 2019 15
- 16. Constructing the matrix GC A T G C 0 0 0 0 0 0 0 G 0 C 0 A 0 T 0 G 0 C 0 Match = 1 Mismatch. = -1 Gap. = -1 1 November 2019 16
- 17. Contd.. G C 0 -1-2 G -1 1 X C -2 Y For X : Top: (-2)+(-1) = (-3) Left: (+1)+(-1) = (0) Top-Left: (-1)+(-1) = (-2) For Y : Top: (1)+(-1) = (0) Left: (-2)+(-1) = (-3) Top-Left: (-1)+(-1) = (-2) The highest value for X and Y is 0, thus it is entered into the cell. i.e X = O; Y = 0 G C 0 -1 -2 G -1 1 0 C -2 0 1 November 2019 17
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- 19. Alignment Rules: Same as ofNeedleman- Wunsch algorithm 1 November 2019 19
- 20. Difference between theprocedure of S-W and N-W algorithm 1 November 2019 20
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- 23. Fig :- Embosshomepage 1 November 2019 23
- 24. Fig 2:- Enteringthe sequence to be compared in N-W algorithm 1 November 2019 24
- 25. Fig 4:- Proteinalignment result 1 November 2019 25
- 26. When comparing 2sequences it is Pairwise sequence alignment (nucleic acids or protein) When comparing more than 2 sequence it is Mulitiple sequence alignment (nucleic acids or protein) 1 November 2019 26
- 27. Contd… Pairwise sequencealignment is concerned with comparing 2 DNA or 2 Amino acids sequences For ex. BLASTn :- for nucleotide sequence BLASTp :- for protein sequence 1 November 2019 27
- 28. BLAST isa Basic Local Alignment Search Tool. Used for comparing primary biological information viz, –Amino acid sequences of protein –Nucleotide of DNA or RNA sequences BLASTn and BLASTp is particularly used for comparing nucleotide sequence and protein sequence respectively1 November 2019 28
- 29. 1 November 201929 Fig 6:- Result of Paralichthys olivaceus in BLASTn
- 30. 1 November 201930 Fig 7:- Sequence producing significant alignment
- 31. 1 November 201931 Fig 8:- Sequence alignment of Paralichthys olivaceus
- 32. Searching largesequences for matches Characterize newly sequenced genes or gene products Molecular distance of evolution between species 1 November 2019 32
- 33. REFERENCE Introduction ofNeedleman-wunsch and smith waterman algorithm David Mount;“Bioinformatics sequence and genome analysis”,chp 3;pp53 Needleman,S.B.and wunsch,C.D.(1970), “A general method applicable to the search for similarities in the amino acid sequence of two proteins”, J.Mol.Biol.,vol,48,pp 443-453. 1 November 2019 33
- 34. Contd.. Smith, T.t.&Waterman,M.S.(1981), “Identification of common molecular subsequences”, - J.Mol.Biol.,vol.147,pp195-197 Tools used for sequence alignment (https://www.omictools.com) (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3446 765/) 1 November 2019 34
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