BIMM 120 Lecture Notes - Lecture 3: Phylogenetic Tree, Fastq Format, Neighbor Joining
26 Oct 2018
School
Department
Course
Professor
Document Summary
How to construct a phylogenetic tree: sequencing, human genome has 47 pieces (23 copies of chromosomes and 1 mitochondrial. We want the dna sequence of all 47 pieces to determine closest relatives. In the real world, perform short-gap sequencing: break gene into fragments and sequence the smaller portions of dna. After sequencing all fragments, can gain the sequence of the entire gene through reconstruction and alignment: de novo genome assembly: reconstruct the original genome from the sequence (cid:396)eads o(cid:374)l(cid:455). Millio(cid:374)s of sho(cid:396)t se(cid:395)ue(cid:374)(cid:272)es (cid:858)(cid:396)eads(cid:859) -> a fe(cid:449) lo(cid:374)g se(cid:395)ue(cid:374)(cid:272)es (cid:858)(cid:272)o(cid:374)tigs(cid:859) The more distant the ancestor, the lower the probability becomes (less confident) If the bootstrap value is lower than 75, there is no accuracy in the relationship between the organisms: clicker question: we can use the 16s rrna gene to look for which organisms, bacteria and archaea, not fungi. If gene has been transferred vertically, the organism tree = gene tree.
