In his laboratory work, the principal investigator does not know enough about the use and interpretation of sequence alignments. Upon arrival, the investigator meets with you and asks your opinion in different scenarios:

A. You have two proteins with a remote and weak similarity. You know their amino acid sequences and also the original DNA sequences. Why would you expect a better alignment using the protein sequences?

B. You have 3 sequences, A, B, C. Sequences B and C are both related to A, but you can't have a good alignment when you align B and C. Why can this be? You can include a diagram if it is easier to explain.

C. You have 2 proteins with 20% sequence identity and I ask if this is a significant result. What other information do you think you need to properly answer the question?