02.08.2013 Views

Algorithms on Sequences

Algorithms on Sequences

Algorithms on Sequences

SHOW MORE
SHOW LESS

You also want an ePaper? Increase the reach of your titles

YUMPU automatically turns print PDFs into web optimized ePapers that Google loves.

Principle of the heuristics (3)<br />

3 – Each hit is « extended » to produce an<br />

alignment<br />

hit<br />

Sequence of the bank<br />

AATCGGATTGCATAA<br />

ATGGACTGGC<br />

Query sequence<br />

alignment<br />

ATCGGATTG<br />

|| ||| ||<br />

AT.GGACTG<br />

Speed Gain of the heuristics<br />

• Example : 2 sequences of DNA of size 1000<br />

• Dynamic Programming :<br />

– 1000 x 1000 = 10 6 matrix-cells<br />

• Heuristics with W = 8<br />

– statistically :<br />

nb of hits = 10 6 x (1 / 4 8 ) = 15 (1 for W=10)<br />

– 1000 search in the dicti<strong>on</strong>nary (10 x 10 3 operati<strong>on</strong>s)<br />

– 15 extensi<strong>on</strong>s (15 x 10 3 operati<strong>on</strong>s)<br />

• Gain : 10 6 / 2.5 x 10 4 = 40 (87 for W=10)

Hooray! Your file is uploaded and ready to be published.

Saved successfully!

Ooh no, something went wrong!