Bioinformatics 2: Introduction pt. 2

Question 1

Why are python and perl human readable?

Answer 1

High level: Written language is readable by humans -> computer runs ‘interpreter’ to convert the readable language to something it can understand

Question 2

Purpose of a PSI-BLAST search? What does it stand for?

Answer 2

Position Specific Iterative - BLAST

Finds related proteins

Question 3

How does a PSI-BLAST search work?

Answer 3

Use Protein A as a query

Protein B is detected using Protein A as a query

Iterative searching helps detect more distant relatives with intermediate sequences

i. e Protein C is detected using Protein B as a query
- > process repeated

Use of a position sequence scoring matrix (PSSM) to rank similarities

Question 4

Do amino acid substitutions have an equal proportion of occurrence

Answer 4

No - more chemically similar amino acids are more likely to have been substituted and conserved

Question 5

What is the primary database for protein structures?

Answer 5

wwPDB

- mirrored between 3 sites