SLIDE 1
Sequence Alignment
Mark Voorhies 4/24/2012
Mark Voorhies Sequence Alignment
Exercise: Transforming sequences
1
Sequence Alignment Mark Voorhies 4/24/2012 Mark Voorhies Sequence - - PowerPoint PPT Presentation
Sequence Alignment Mark Voorhies 4/24/2012 Mark Voorhies Sequence - - PowerPoint PPT Presentation
Sequence Alignment Mark Voorhies 4/24/2012 Mark Voorhies Sequence Alignment Exercise: Transforming sequences 1 Write a function to return the antisense strand of a DNA Why compare sequences? Mark Voorhies Sequence Alignment Why compare
SLIDE 2
SLIDE 3
Why compare sequences?
Mark Voorhies Sequence Alignment
SLIDE 4
Why compare sequences?
To find genes with a common ancestor To infer conserved molecular mechanism and biological function To find short functional motifs To find repetitive elements within a sequence To predict cross-hybridizing sequences (e.g. in microarray design) To predict nucleotide secondary structure
Mark Voorhies Sequence Alignment
SLIDE 5
Whiteboard Image
Mark Voorhies Sequence Alignment
SLIDE 6
Nomenclature
Homologs heritable elements with a common evolutionary
- rigin.
Mark Voorhies Sequence Alignment
SLIDE 7
Nomenclature
Homologs heritable elements with a common evolutionary
- rigin.
Orthologs homologs arising from speciation. Paralogs homologs arising from duplication and divergence within a single genome.
Mark Voorhies Sequence Alignment
SLIDE 8
Nomenclature
Homologs heritable elements with a common evolutionary
- rigin.
Orthologs homologs arising from speciation. Paralogs homologs arising from duplication and divergence within a single genome. Xenologs homologs arising from horizontal transfer. Onologs homologs arising from whole genome duplication.
Mark Voorhies Sequence Alignment
SLIDE 9
Dotplots
1
Unbiased view of all ungapped
SLIDE 10
Dotplots
1
Unbiased view of all ungapped
SLIDE 11
Types of alignments
Global Alignment Each letter of each sequence is aligned to a letter or a gap (e.g., Needleman-Wunsch) Local Alignment An optimal pair of subsequences is taken from the two sequences and globally aligned (e.g., Smith-Waterman)
Mark Voorhies Sequence Alignment
SLIDE 12
Exercise: Scoring an ungapped alignment
s =
SLIDE 13
Exercise: Scoring an ungapped alignment
s =
SLIDE 14
Exercise: Scoring an ungapped alignment
s =
SLIDE 15
Exercise: Scoring an ungapped alignment
s =
SLIDE 16
Exercise: Scoring a gapped alignment
1
Given two equal length gapped sequences (where “-”
SLIDE 17
Exercise: Scoring a gapped alignment
1
Given two equal length gapped sequences (where “-”
SLIDE 18
Homework
1