SLIDE 1
2003.03.01 FFT sequence analysis
2
FFT analysis of DNA sequences Harvey Lab Group Meeting March 1, - - PowerPoint PPT Presentation
FFT analysis of DNA sequences Harvey Lab Group Meeting March 1, - - PowerPoint PPT Presentation
FFT analysis of DNA sequences Harvey Lab Group Meeting March 1, 2004 Russell Hanson 2 Nave string search: FFT sequence analysis implementation 2003.03.01 3 Alignments local and global FFT sequence analysis 2003.03.01 BLAST Two
SLIDE 2
SLIDE 3
2003.03.01 FFT sequence analysis
3
Alignments local and global
SLIDE 4
2003.03.01 FFT sequence analysis
4
BLAST
Two steps: 1) Hash
2) Lookup table
It encodes all the 8-mers as numbers, then it encodes
the search string (i.e. chromosome sequence fragment), then it shifts the 8-mers along the search string, building a lookup table of 8-mers and their locations in the search
- string. For any subsequent search, therefore, you need
- nly compare the hash values of the query string with
the lookup table (avoiding working with the search string ever again).
SLIDE 5
2003.03.01 FFT sequence analysis
5
Fourier transforms
SLIDE 6
2003.03.01 FFT sequence analysis
6
Fourier transforms II
This is a matrix vector multiplication, which takes O(n)
- perations.
SLIDE 7
2003.03.01 FFT sequence analysis
7
Convolution & correlation
SLIDE 8
2003.03.01 FFT sequence analysis
8
Convolution & correlation II
SLIDE 9
2003.03.01 FFT sequence analysis
9
FFT Convolution equation
SLIDE 10
2003.03.01 FFT sequence analysis
10
Convolution theorem
SLIDE 11
2003.03.01 FFT sequence analysis
11
Base vector encodings
SLIDE 12
2003.03.01 FFT sequence analysis
12
C Language implementation
SLIDE 13
2003.03.01 FFT sequence analysis
13
Results
SLIDE 14
2003.03.01 FFT sequence analysis
14
PSSMs
SLIDE 15
2003.03.01 FFT sequence analysis
15
Shift-and algorithm
SLIDE 16
2003.03.01 FFT sequence analysis
16
MAFFT – Multi-Alignment FFT
SLIDE 17
2003.03.01 FFT sequence analysis
17
FFT for global alignment
SLIDE 18
2003.03.01 FFT sequence analysis
18