How is the Position SOecific Scoring Matrix (PSSM) generated?
MSA of hits from the first iteration of PSI-BLAST; PSSM used in the second iteration
Give 3 ways MSAs can give information on protein structure and function?
- Identify novel conserved domains
- Explore novel motifs and domains
- If crystal strucure is known, model others that are homologous (Homology Modelling)
Why is MSA more computationally intensive than pairwise sequence alignment?
What is the central problem of protein structure?
Sequence doesn't predict structuer
In what way is progressive alignment a compromise?
Compromise between speed and accuracy
Why is progressive alignment the prevailing strategy?
It's fast and effective
What is the 2-part strategy used in progressive alignments?
- Exhaustive pairwise alignments find closely related sequences
- Related sequences are progressively aligned by clustering
Give 3 features of the Hidden Markov Model
- Model is hidden; only output is visible
- Doesn't require pre-existing alignment; generates amino acid probabilities and aligns sequences
- Probabilities adjusted, when the model is run, to generate most likely path
List 3 reasons for performing multiple sequence alignment (MSA)?
- Finding other related sequences
- Genome sequencing (assembly)
- Phylogenetic analysis
How can Multiple Alignments (MAs) be used in phylogeny?
MAs of highly conserved sequences can be used to determine evolutionary relationships
If given a Hidden Markov Model (HMM) of a sequence famiy and a query sequence, what can you calculate?
The probability that the HMM could emit the query; if this probability is high then query is likely a member of family
What does Multiple Sequence Alignment (MSA) of homologius/orthologous genes reveal?
- Conserved nad variable regions
- Domain structure of proteins
- Likelystructure of novel protiens (Homology modelling)
What 4 stages are involved in protein homology modelling?
- Align query protein with most similar sequence that has an X-ray crystal structure
- Superimpose, in 3 dimensions, the 2 structures; query and known
- Test the model (positions of backbone carbons, side chains)
- Propose model of query protein structure
What might conserved protein domains correspond to?
Protein secondary structures