Hmmer mul1ple sequence alignment clustalw fsa genomic

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Unformatted text preview: nments Accoun1ng for Gaps Score for a gap of length x is  ­(ρ + σx), where ρ >0 is the penalty for introducing a gap: gap opening penalty ρ will be large rela1ve to σ: gap extension penalty because you do not want to add too much of a penalty for extending the gap. Affine Gap Penal1es •  Gap penal1es: –  ­ρ ­σ when there is 1 indel –  ­ρ ­2σ when there are 2 indels –  ­ρ ­3σ when there are 3 indels, etc. –  ­ρ ­ x σ ( ­gap opening  ­ x gap extensions) •  Somehow reduced penal1es (as compared to naïve scoring) are given to runs of horizontal and ver1cal edges Heuris1c Algorithms •  Make reasonable assump1ons about nature of sequence alignments and try out only “most likel...
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This note was uploaded on 02/10/2014 for the course CS 680 taught by Professor Staff during the Fall '08 term at Colorado State.

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