8/31/07 C.Bystroff 1
BIOL 6961 Fall 2007
• 8/31: Sequence Alignment
– inferences, methods, significance, editing
• 9/5: Database searching
– methods, e-values, GenBank files
• 9/7: Fitting data
– parametric space, correlations, training
and testing
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Sequence Alignment: Methods, Significance, and Optimal Alignment Scoring, Study notes of Cancer Cytogenetics
An overview of sequence alignment, including methods such as pairwise alignments, multiple alignments, and dynamic programming algorithms like the smith-waterman method. It also covers the significance of sequence similarity and the calculation of optimal alignment scores.
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8/31/07 C.Bystroff 1
BIOL 6961 Fall 2007
• 8/31: Sequence Alignment
- inferences, methods, significance, editing
• 9/5: Database searching
- methods, e-values, GenBank files
• 9/7: Fitting data
- parametric space, correlations, training
and testing
8/31/07 C.Bystroff 2
Pairwise alignments
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AAAGA GATTCTGC TAGCGGT CGG
AGAGATGCTGCAGCGAGTCGGCC
Plant. Bug. Aligning two sequences An alignment is a one-to-one association, or a set of one- to-one associations. What does it mean? What kinds of associations are allowed?
8/31/07 C.Bystroff 5 Venn Diagram -- two meanings of "aligned", for proteins. (A) have a common ancestor (B) superimpose in space TG CTA (^) TGCAA TG CTA Aligned positions.... some positions have a common ancestor but don’t superimpose in space evolution conserves structure, mostly some positions that superimpose in space didn’t have a common ancestor (convergent evolution).
8/31/07 C.Bystroff 7
AAAGA GATTCTGC TAGCG.G TCGG..
..AGA GATGCTGC .AGCGAG TCGGCC
Plant. Bug. Columns denote association Dots or dashes are spacers, or gaps. The sequence with a gap character has a deletion. The sequence aligned to a gap character has an insertion. Characters in the same column are aligned (or matched ) Matched characters can be identity matches or mutations.
Bird. ..AG. GAAGCTGC AAGCCAG TCGGTC
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The optimal alignment
• "The alignment" can be any set of one-
to-one associations between
characters, but it generally means the
best (or optimal ) alignment.
• The best alignment is the one that
assumes the fewest mutations , or
smallest evolutionary distance.
• To find the optimal alignment, we must
define evoutionary distance.
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The optimal alignment
- Simple similarity score: Identity match = +1 point mismatch = -1 points gap = -1 points
- Optimal alignment = The highest-scoring alignment given the similarity score.
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Computing pairwise
alignments
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AAAGA GATTCTGC TAGCGGT CGG
A G A G A T G C T G C A G C G A G T C G G C C
Dot plot:
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AAAGA GATTCTGC TAGCGGT CGG
A G A G A T G C T G C A G C G A G T C G G C C
Dot plot:
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AAAGA GATTCTGC TAGCGGT CGG
A G A G A T G C T G C A G C G A G T C G G C C
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AAAGA GATTCTGC TAGCGGT CGG
A G A G A T G C T G C A G C G A G T C G G C C
blocks gaps insertion, A deletion, T mutation, T->G
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AAAGA GATTCTGC TAGCGGT CGG
A G A G A T G C T G C A G C G A G T C G G C C
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