Lecture 11 Flashcards Preview

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Flashcards in Lecture 11 Deck (14):
1

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

1

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)

1

Why is MSA more computationally intensive than pairwise sequence alignment?

Scaling

2

What is the central problem of protein structure?

Sequence doesn't predict structuer

3

In what way is progressive alignment a compromise?

Compromise between speed and accuracy

4

Why is progressive alignment the prevailing strategy?

It's fast and effective

5

What is the 2-part strategy used in progressive alignments?

  • Exhaustive pairwise alignments find closely related sequences
  • Related sequences are progressively aligned by clustering

6

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

8

List 3 reasons for performing multiple sequence alignment (MSA)?

  • Finding other related sequences
  • Genome sequencing (assembly)
  • Phylogenetic analysis

9

How can Multiple Alignments (MAs) be used in phylogeny?

MAs of highly conserved sequences can be used to determine evolutionary relationships

10

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

12

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)

13

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

14

What might conserved protein domains correspond to?

Protein secondary structures