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Bit score S' Score S depends on the substitution table What if we want table-independent score? E=mn2 −S' where S'= E=Kmne −S S−ln K ln 2
Why does the BLAST work? Relevant riddle Are there at least 2 people in Amsterdam with the same number of hairs? – At most 500 000 hairs on each head – 700 000 people living in Amsterdam
Page 1 and 2: Alignments BLAST, BLAT
Page 3 and 4: The amount of genetic information i
Page 5 and 6: Sequence searching - challenges Ex
Page 7 and 8: Sequence searching - definition We
Page 9 and 10: Database Search Algorithms: Sensiti
Page 11 and 12: What means well conserved for BLAST
Page 13 and 14: BLAST, Step 1: Preprocess the query
Page 15 and 16: BLAST, Step 2: Find ¨exact¨ match
Page 17 and 18: Gapped BLAST (now standard) gapped
Page 19 and 20: Gapped BLAST v BLAST We end up wit
Page 21 and 22: PSI-BLAST Position-Specific Iterat
Page 23 and 24: Constructing a profile Take signif
Page 25 and 26: BLAT, Step 1: Preprocess the databa
Page 27 and 28: Hashing - examples T9 Predictive T
Page 29 and 30: BLAT, Step 2: Hit criteria 1)Prepro
Page 31 and 32: BLAT, Step 3: Identifying homologou
Page 33 and 34: How to detect homology? Take the s
Page 35 and 36: Best Local Alignments by chance Cr
Page 37 and 38: Expected number of aligns E-value:
Page 39: Deriving K, L The above eq is theo
Page 43 and 44: Why does the BLAST work? Average ca
Page 45 and 46: Why does the BLA[S]T work? Forget
Page 47 and 48: Expected sensitivity Q - query siz

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