BIO 3102 Lecture Notes - Lecture 3: Gap Penalty, Clustal, Indel
29 Aug 2016
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If closely related (short time period) high probability only one change at any given site: but if distant may have been multiple substitutions (hits) at a site, can use algorithms to correct for this, 2. Synonymous vs. non-synonymous: single step: point mutation or multiple alleles, multiple steps: ccc cca & cac caa, the pathway to get to caa, the more likely pathway will have a synonymous change, 2. Alignment of sequences for comparative analysis: 1. If sequences very similar and no (or few) gaps: 2. By sequences distance methods: use algorithms which minimize mismatches and gaps, gap penalty > mismatch penalty, because nt sub is typically more probable dna change than indel, at least within protein-coding sequences. Multiple sequence alignments: clustal omega, muscle, go to evolutionary tree and find similarly diverged organisms, blocks of high identity, so confident alignment even though there is an indel, indel scores as one evolutionary event.
