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Hit criteria<br />
Extends the alignment only if there are<br />
close two hits on the same diagonal<br />
– sensitivity would drop without lowering T<br />
– reduces extensions (90% time is spend<br />
on extensions)<br />
Gapped local alignments are computed<br />
query<br />
pos<br />
– increased sensitivity allows us raise T<br />
– raising T speeds up the search<br />
close hit, same diag<br />
dbpos<br />
1)Preprocess<br />
2)Scan<br />
3)Extend
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