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 Naïve string search: FFT sequence analysis implementation 2003.03.01

3 Alignments local and global FFT sequence analysis 2003.03.01

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 only compare the hash values of the query string with the lookup table (avoiding working with the search string ever again). 4 2003.03.01 FFT sequence analysis

5 FFT sequence analysis Fourier transforms 2003.03.01

Fourier transforms II � This is a matrix vector multiplication, which takes O(n) operations. 6 2003.03.01 FFT sequence analysis

7 Convolution & correlation FFT sequence analysis 2003.03.01

8 Convolution & correlation II FFT sequence analysis 2003.03.01

9 FFT Convolution equation FFT sequence analysis 2003.03.01

10 Convolution theorem FFT sequence analysis 2003.03.01

11 Base vector encodings FFT sequence analysis 2003.03.01

12 C Language implementation FFT sequence analysis 2003.03.01

13 FFT sequence analysis Results 2003.03.01

14 FFT sequence analysis PSSMs 2003.03.01

15 FFT sequence analysis Shift-and algorithm 2003.03.01

16 MAFFT – Multi-Alignment FFT FFT sequence analysis 2003.03.01

17 FFT for global alignment FFT sequence analysis 2003.03.01

18 Group-group alignment FFT sequence analysis 2003.03.01