Molecular Biology Information: Protein Sequence
Step 1 -- Make a Dot Plot (Similarity Matrix)
Step 2 --
Start Computing the Sum Matrix
Step 6 -- Alternate Tracebacks
Step 2 -- Computing the Sum Matrix with Gaps
Key Idea in Dynamic Programming
Similarity (Substitution) Matrix
Amino Acid Frequencies of Occurrence
Principles of Scoring Matrix Construction, in detail
Principles of Scoring Matrix Construction, in detail #2
Principles of Scoring Matrix Construction, in detail #3
Different Matrices are Appropriate at Different Evolutionary Distances
Change in Matrix with Ev. Dist.
Other Matrices:
How to score the exchange of two amino acids in an alignment?
Modifications for Local Alignment
Transitive Sequence Comparison
Progressive Multiple Alignments
Problems with Progressive Alignments
Popular Multiple Alignment Programs
Profiles formula for
position
M(p,a)
Profiles formula for
entropy
H(p,a)
Prosite Pattern -- EGF like pattern
EGF Profile Generated for SEARCHWISE
Example:
simple fully interconnected model (N=3)
Scoring by Brute Force method:
Score in Context of Other Scores
Objective is to Find Distant Homologues
What Distribution Really Looks Like
Explicit Form of the P-value in terms of Extreme Value Distribution
Use Sequence Scores to Validate
Significance
Depends
on Database Size
Join together query lookups into diagonals and then a full alignment
Analytic Score Formalism for Blast
Practical Issues on DNA Searching
General Protein Search Principles
What secondary structure prediction tries to accomplish?
How to use GES to predict proteins
Ex. P(i,a) probability that residue i has secondary structure a
Statistics Based
Methods:
Persson & Argos
Refinements: Charge on the Outside, Positive Inside Rule
Types of Secondary Structure Prediction Methods
GOR Semi-parametric Improvements
Additional Features of DNA sequences in Genomes