Consider the possible scoring systems and then answer the questions below. Which

Question

Consider the possible scoring systems and then answer the questions below.

Which scoring system above is most appropriate for an alignment involving


a) two homologous proteins that are expected to have a very high overall similarity



b) two homologous proteins that are distantly related and may have a relatively low similarity (due primarily to missense mutations)



c) two different proteins where the goal is to identify small functional regions (domains) of very high similarity.

Scoring System Substitution Matrix Gap Opening Penalty Gap Extension Penalty #1 BLOSUM90 2 1 #2 BLOSUM45 2 1 #3 BLOSUM90 10 1 #4 BLOSUM45 10 1

Explanation / Answer

a) 90 represents 90% similarity so it is used for closely related proteins. If the gap opening penalty is high it affects the score. So penalty should be less.

b) 45 represents 45% similarity so it is used for distantly related proteins.

c) Domains of high similarity is possible only when proteins are closely related.

#1 BLOSUM90 2 1

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