BI - Penalities for the Presence of Gaps

Questions

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IMPORTANTE

IMPORTANTE Indel Events: (INsertion/DELetion)

IMPORTANTE Penalities for the Presence and the Length of a Gap The scoring function has to reward alignments, that are most plausible from the evolutionary point of view. ~Ex.: an indel event creating a gap of 2 nucelotides (consecutives), is more probable than 2 indel event creating 2 gaps in different parts of the DNA. The “loss function” can be: -2 for a gap, -1 for each gap after the first, and +1 for each alignment, +0 for each missmatch

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Slides with Notes

IMPORTANTE Indel Events: (INsertion/DELetion)

IMPORTANTE Penalities for the Presence and the Length of a Gap The scoring function has to reward alignments, that are most plausible from the evolutionary point of view. ~Ex.: an indel event creating a gap of 2 nucelotides (consecutives), is more probable than 2 indel event creating 2 gaps in different parts of the DNA. The “loss function” can be: -2 for a gap, -1 for each gap after the first, and +1 for each alignment, +0 for each missmatch