Table of ContentsBIOINFORMATICS Sequences Sequence Topics (Contents) Molecular Biology Information: Protein Sequence Aligning Text Strings Dynamic Programming Step 1 -- Make a Dot Plot (Similarity Matrix) A More Interesting Dot Matrix Step 2 -- Start Computing the Sum Matrix Step 3 -- Keep Going Step 4 -- Sum Matrix All Done Step 5 -- Traceback Step 5 -- Traceback Step 6 -- Alternate Tracebacks Suboptimal Alignments Suboptimal Alignments II Gap Penalties Step 2 -- Computing the Sum Matrix with Gaps All Steps in Aligning a 4-mer Key Idea in Dynamic Programming Similarity (Substitution) Matrix How to score the exchange of two amino acids in an alignment? Where do matrices come from? 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. The BLOSUM Matrices Local vs. Global Alignment Modifications for Local Alignment Local vs. Global Alignment Transitive Sequence Comparison Multiple Sequence Alignments Progressive Multiple Alignments Problems with Progressive Alignments Popular Multiple Alignment Programs C1Q Clustal Alignment Profiles Motifs HMMs Motifs Prosite Pattern -- EGF like pattern Profiles EGF Profile Generated for SEARCHWISE HMMs Modules The Score Score in Context of Other Scores P-value in Sequence Matching Objective is to Find Distant Homologues P-values What Distribution Really Looks Like EVD Fits Extreme Value vs. Gaussian EVD #2 Explicit Form of the P-value in terms of Extreme Value Distribution Use Sequence Scores to Validate Significance Depends on Database Size Low-Complexity Regions Computational Complexity FASTA Join together query lookups into diagonals and then a full alignment Basic Blast Blast: Extension of Hash Hits Blasting against the DB Analytic Score Formalism for Blast Blast2: Gapped Blast Blast2: Gapped Blast PSI-Blast Practical Issues on DNA Searching General Protein Search Principles Overview What secondary structure prediction tries to accomplish? Some TM scales: GES KD How to use GES to predict proteins Graph showing Peaks in scales Removing Signal sequences Ex. Pr(S) probability that residue j has secondary structure i Statistics Based Methods: Persson & Argos Refinements: Charge on the Outside, Positive Inside Rule Refinements: MaxH GOR: Simplifications Basic GOR Directional Information Types of Residues GOR IV Assessment Training and Testing Set Is 100% Accuracy Possible? Types of Secondary Structure Prediction Methods GOR Semi-parametric Improvements Multiple Sequence Methods DSC -- an improvement on GOR Neural Networks More NN Yet more methods…. Mail Servers and Web Forms Additional Features of DNA sequences in Genomes Genetic Code Splicing Alternative Splicing: Multiple Proteins from One Gene Promotors References References References References |
Author: Office97
Email: Mark.Gerstein@yale.edu Home Page: http://bioinfo.mbb.yale.edu |