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BLAT, Step 2:<br />
Hit criteria<br />
1)Preprocess<br />
2)Scan<br />
3)Extend<br />
In a constant time we can get the<br />
sequences with a certain k-word<br />
relaxing hit definition -> improve<br />
sensitivity<br />
– allow imperfect hits<br />
• costly, huge hash grows a few times!<br />
➔ shorten k (would lead to FP), but<br />
expect two hits (see BLAST)
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