Multiple Alignments, Substitution Matrices, Profiles and HMM-s

(Hedi Hegyi)

Multiple Alignments

Multiple Alignments as Practically Useful Methods

A Phylogenetic Tree with a Universal Ancestor

Progressive Multiple Alignments

Problems with Progressive Multiple Alignments
Amino Acid Substitution Matrices

They can be constructed in several different ways -eg. based on their physico-chemical properties

The Calculation of the Dayhoff  (PAM) Matrices

A Frequently Used Dayhoff Matrix

The BLOSUM Matrices

How to construct an alignment:

Take a  multiple FASTA fomatted file

Run  CLUSTALW and get a multiple alignment for the C1Q protein family

Profiles and Motifs

The EGF  protein domain

Profile for the EGF domain

A profile search program: SEARCHWISE output  for EGF

Pfam - Protein Famillies with Hidden Markov Models

Pfam documentation for the EGF domain

SwissPfam - The domain organization of a Swissprot entry, CAMA_CHICK according to Pfam

Secondary Structure Prediction  from Multiple Alignments with PredictProtein