Computational Biology
Scribe Notes for Class 19
June 16, 2000
Scribe: C. Wingrave
Today's Handouts and Announcements
-
Handout - Dynamic Programming Algorithms for Biological Sequence Comparison
Today's Topics
- Evolution -> Speciation, variants in proteins, divergence
- Relationships -> graphs, trees
- Phylogenic Trees (PT)
- leaves are known objects
- interior nodes are intermediary objects or unknowns
- Information we have for PTs
- character state matrix
- character - characteristic from some finite set of states
| c1 | c2 | c3 | c4 | c5 |
| A | 1 | 1 | 0 | 0 | 0 |
| B | 0 | 0 | 1 | 0 | 1 |
| C | 1 | 1 | 0 | 0 | 1 |
| D | 0 | 1 | 1 | 1 | 0 |
| E | 1 | 1 | 0 | 0 | 1 |
- ordered vs unordered
- assume characters are independent
- assume 1 common ancester (if ordered)
- distance matrix
- Edit distance -> count of substitutions, insertions and deletions between two sequences i and j
- Sequences
ACA___ATG
TCAACTATC
ACAC__AGC
AGA___ATC
ACCG__ATC
| D = | | | 0 | 5 | 3 | 2 | 3 | | |
| | | 5 | 0 | 4 | 5 | 4 | | |
| | | 3 | 4 | 0 | 3 | 3 | | |
| | | 2 | 5 | 3 | 0 | 3 | | |
| | | 3 | 4 | 3 | 3 | 0 | | |
- What can go wrong
- reversals: h->j->h
- convergence: two distant species have same state of character
- Perfect Phylogeny Problem
- Instance: set O of n objects, a set C of m characteristics, at most r states per character, character state table
- Question: Is there a perfect phylogeny for O?
- NP-Hard for unordered and P for ordered
Today's Sources