Sequence alignments Genetic sequences change over time mutation - PowerPoint PPT Presentation

Sequence alignments

Genetic sequences change over time mutation deletion mutation LRGGD LRGD LRCD ARCD time Relationship between original and final sequence: LRGGD LRGGD or AR-CD ARC-D

In practice: we only know sequences from extant organisms human LRGDDC ancestor mouse LGDCC

We need to align these sequences to compare them human mouse LRGDDC LGDCC LRGDDC LRGDDC- LRGDDC L-GDCC L-GD-CC -LGDCC Which alignment is correct?

We need to score the alignment Example: score = 1+0+1+1-1+1 LRGDDC = 3 • match = +1 L-GDCC • mismatch = -1 score = 1+0+1+1+0+1+0 LRGDDC- • gap = 0 = 4 L-GD-CC score = 0-1+1+1-1+1 LRGDDC = 1 -LGDCC

We need to score the alignment Example: score = 1-2+1+1-1+1 LRGDDC = 1 • match = +1 L-GDCC • mismatch = -1 score = 1-2+1+1-2+1-2 LRGDDC- • gap = -2 = -2 L-GD-CC score = -2-1+1+1-1+1 LRGDDC = -1 -LGDCC

We often score by amino-acid similarity BLOSUM62 Matrix score = log p ij p i p j http://commons.wikimedia.org/wiki/File:BLOSUM62.gif

Gaps in alignments are called “indels” LRGDDC L-GDCC indel

How do we find the best alignment given a scoring system? Global alignment: Needleman-Wunsch algorithm Example: align GCAT and GAT Scoring: match = 1, mismatch = -1, gap = -1 - G C A T - G A T

How do we find the best alignment given a scoring system? Global alignment: Needleman-Wunsch algorithm Example: align GCAT and GAT Scoring: match = 1, mismatch = -1, gap = -1 Alignment: - G C A T - - 0 - G A T

How do we find the best alignment given a scoring system? Global alignment: Needleman-Wunsch algorithm Example: align GCAT and GAT Scoring: match = 1, mismatch = -1, gap = -1 Alignment: - G C A T 0 -1 -G - -- G A T

How do we find the best alignment given a scoring system? Global alignment: Needleman-Wunsch algorithm Example: align GCAT and GAT Scoring: match = 1, mismatch = -1, gap = -1 Alignment: - G C A T 0 -1 -2 -GC - --- G A T

How do we find the best alignment given a scoring system? Global alignment: Needleman-Wunsch algorithm Example: align GCAT and GAT Scoring: match = 1, mismatch = -1, gap = -1 Alignment: - G C A T 0 -1 -2 -3 -4 -GCAT - ----- G A T

How do we find the best alignment given a scoring system? Global alignment: Needleman-Wunsch algorithm Example: align GCAT and GAT Scoring: match = 1, mismatch = -1, gap = -1 Alignment: - G C A T 0 -1 -2 -3 -4 -- - -G -1 G A T

How do we find the best alignment given a scoring system? Global alignment: Needleman-Wunsch algorithm Example: align GCAT and GAT Scoring: match = 1, mismatch = -1, gap = -1 Alignment: - G C A T 0 -1 -2 -3 -4 ---- - -GAT -1 G A -2 -3 T

How do we find the best alignment given a scoring system? Global alignment: Needleman-Wunsch algorithm Example: align GCAT and GAT Scoring: match = 1, mismatch = -1, gap = -1 - G C A T 0 -1 -2 -3 -4 - -1 ? G A -2 -3 T

How do we find the best alignment given a scoring system? Global alignment: Needleman-Wunsch algorithm Example: align GCAT and GAT Scoring: match = 1, mismatch = -1, gap = -1 Alignment: - G C A T 0 -1 -2 -3 -4 -G- - --G -1 -2 G A -2 -3 T

How do we find the best alignment given a scoring system? Global alignment: Needleman-Wunsch algorithm Example: align GCAT and GAT Scoring: match = 1, mismatch = -1, gap = -1 Alignment: - G C A T 0 -1 -2 -3 -4 --G - -G- -1 -2 G A -2 -3 T

How do we find the best alignment given a scoring system? Global alignment: Needleman-Wunsch algorithm Example: align GCAT and GAT Scoring: match = 1, mismatch = -1, gap = -1 Alignment: - G C A T 0 -1 -2 -3 -4 -G - -G -1 1 G A -2 -3 T

How do we find the best alignment given a scoring system? Global alignment: Needleman-Wunsch algorithm Example: align GCAT and GAT Scoring: match = 1, mismatch = -1, gap = -1 Alignment: - G C A T 0 -1 -2 -3 -4 -GC - -G- -1 1 0 G A -2 -3 T

How do we find the best alignment given a scoring system? Global alignment: Needleman-Wunsch algorithm Example: align GCAT and GAT Scoring: match = 1, mismatch = -1, gap = -1 Alignment: - G C A T 0 -1 -2 -3 -4 -G- - -GA -1 1 0 G A -2 0 -3 T

How do we find the best alignment given a scoring system? Global alignment: Needleman-Wunsch algorithm Example: align GCAT and GAT Scoring: match = 1, mismatch = -1, gap = -1 Alignment: - G C A T 0 -1 -2 -3 -4 -GC- - -G-A -1 1 0 G A -2 0 -1 -3 T

How do we find the best alignment given a scoring system? Global alignment: Needleman-Wunsch algorithm Example: align GCAT and GAT Scoring: match = 1, mismatch = -1, gap = -1 Alignment: - G C A T 0 -1 -2 -3 -4 -G-C - -GA- -1 1 0 G A -2 0 -1 -3 T

How do we find the best alignment given a scoring system? Global alignment: Needleman-Wunsch algorithm Example: align GCAT and GAT Scoring: match = 1, mismatch = -1, gap = -1 Alignment: - G C A T 0 -1 -2 -3 -4 -GC - -GA -1 1 0 G A -2 0 0 -3 T

How do we find the best alignment given a scoring system? Global alignment: Needleman-Wunsch algorithm Example: align GCAT and GAT Scoring: match = 1, mismatch = -1, gap = -1 - G C A T 0 -1 -2 -3 -4 - -1 1 0 -1 -2 G A -2 0 0 1 0 -3 -1 -1 0 2 T

How do we find the best alignment given a scoring system? Global alignment: Needleman-Wunsch algorithm Example: align GCAT and GAT Scoring: match = 1, mismatch = -1, gap = -1 Alignment: - G C A T 0 -1 -2 -3 -4 -GCAT - -G-AT -1 1 0 -1 -2 G A -2 0 0 1 0 -3 -1 -1 0 2 T

Needleman-Wunsch algorithm, mathematical form M (0, j ) = j × p first row, p = gap penalty M ( i ,0) = i × p first column ⎛ ⎞ M ( i − 1, j ) + p top ⎜ ⎟ M ( i , j ) = max M ( i , j − 1) + p left ⎜ ⎟ ⎜ ⎟ M ( i − 1, j − 1) + s ( a j , b i ) diagonal ⎜ ⎟ ⎝ ⎠ s ( a j , b i ) = match/mismatch score for sites j and i in sequences a and b

Now try on your own Align ATGCT and ATTACA Scoring: match = 1, mismatch = -1, gap = -1 - A T T A C A - A T G C T

Multiple sequence alignment (MSA)

Software to generate MSAs • MAFFT (very good, very fast) http://mafft.cbrc.jp/alignment/software/ • Clustal Omega (very good, very fast) http://www.ebi.ac.uk/Tools/msa/clustalo/ • PRANK (extremely good, very slow) http://wasabiapp.org/software/prank/