Bioinformatics

Question 1

Different ways to compare sequences of amino acids

Answer 1

Sliding analysis : +10 per match -25 for any gap that is added
Shuffling: Randomizing that sequences to see if the matches are coincidental
Blosum 62: Gap is still -25, though different points are awarded for different matches of amino acids (for instance W-W matches are 11 points, but A-A matches are only 5, while E-C matches are -4)

Question 2

Homologs vs Paralogs vs Orthologs

Answer 2

Homologs = Common Ancestor
Paralogs = Homologs in one species that perform different functions 
Orthologs = Homologs that perform similar functions in separate species