Algorithms on Sequences
Algorithms on Sequences
Algorithms on Sequences
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Sequence comparis<strong>on</strong> and alignments<br />
To compare sequences is to look for alignments<br />
MALVEDNNAVAVSFSEEQEALVLKSWAILKKDSANIALRFFLKIFEVAPSASQMF-SF<br />
: .: :...:: .: ... . ..:: . .. . .. ...:.: .:.:...: .:<br />
MPIV-DTGSVA-PLSAAEKTKIRSAWAPVYSNYETSGVDILVKFFTSTPAAQEFFPKF<br />
search in<br />
a bank<br />
local alignment<br />
(blast)<br />
assembly<br />
of genomes<br />
Today lecture<br />
• Dynamic programming applied to<br />
the comparis<strong>on</strong> of sequences<br />
• Alignments<br />
• Substituti<strong>on</strong> matrices<br />
• Validati<strong>on</strong> of comparis<strong>on</strong> results<br />
• Search heuristics<br />
• Introducti<strong>on</strong> to existing softwares<br />
phylogeny<br />
global alignment
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