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
How to construct an alignment:
Take a multiple FASTA fomatted file
Run CLUSTALW and get a multiple
alignment for the C1Q protein family
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