L5W10_MIC105_ZenPhylo2

L5W10_MIC105_ZenPhylo2 - Zen and the Art of Molecular...

Info iconThis preview shows pages 1–18. Sign up to view the full content.

View Full Document Right Arrow Icon

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
This is the end of the preview. Sign up to access the rest of the document.

Unformatted text preview: Zen and the Art of Molecular Phylogeny Part 2: Building Trees The road to Phylogenetic Nirvana by overcoming the Five Hindrances: Desire Anger Sloth Worry Doubt Sunday, January 10, 2010 Label parts of this tree * Sunday, January 10, 2010 Tree exercise Deepest branch = the branch closest to the outgroup Clades = common ancestor + all decendants Outgroup can be a single sequence, or a group (clade) of sequences Scale bar = #changes/site Sunday, January 10, 2010 Which is the deepest branch in the Crenarchaeota? Hint: closest to the outgroup (Euryarchaeota) Sunday, January 10, 2010 How to build trees Sunday, January 10, 2010 Select reliable data Align Sequence data Working alignment Global multiple alignment Tree Score Evolutionary model Best Trees Evaluate (assumptions) * Sunday, January 10, 2010 BLAST Similarity searching with a huge database Various types of search tools Allows choice of databases Look for homologous sequences (Basic Local Alignment Search Tool) QUERY sequence(s) BLAST database BLAST program BLAST results * Sunday, January 10, 2010 Multiple sequence alignment: taxa in rows homologous positions in columns use gaps or indels to bring homologous positions in alignment % identity? Sunday, January 10, 2010 Sequence alignment = hypothesis Common origin (homology) Descended from fragment of an ancestral genome Compared residues trace back to ancestral sequence * Positional homology (columns) * Sunday, January 10, 2010 Sequence alignment = hypothesis Common origin (homology) Descended from fragment of an ancestral genome Compared residues trace back to ancestral sequence * Positional homology (columns)--> Omit non-homologous regions (uncertain ancestry) * Sunday, January 10, 2010 Manual alignment tricks Use an automated alignment tool to get started Align like things frst (more similar) Use structural inFormation when available * Sunday, January 10, 2010 Manual alignment tricks Use an automated alignment tool to get started Align like things frst (more similar) Use structural inFormation when available indels * Sunday, January 10, 2010 Manual alignment tricks Use an automated alignment tool to get started Align like things frst (more similar) Use structural inFormation when available indels * Sunday, January 10, 2010 Conserved tertiary structure, but not primary structure (sequence) 10% identity 10% identity * Sunday, January 10, 2010 Conserved tertiary structure, but not primary structure (sequence) 10% identity 10% identity Use tertiary structure as alignment guide! * Sunday, January 10, 2010 Secondary Structure: small subunit ribosomal RNA * Sunday, January 10, 2010 A G G A C - G A - U G - C G - C A G G A C - G G - C C - G U - A Primary sequence can change while secondary structure is preserved Watson-Crick base pairing: A-U, G-C (U=uracil in RNAs) Non-W-C base pairing: (U-U, U-C, U-G) * Sunday, January 10, 2010 Sunday, January 10, 2010...
View Full Document

Page1 / 76

L5W10_MIC105_ZenPhylo2 - Zen and the Art of Molecular...

This preview shows document pages 1 - 18. Sign up to view the full document.

View Full Document Right Arrow Icon
Ask a homework question - tutors are online