1) Say a 89 nt duplication happened around nucleotide number 200 of the wild-type gene.
a. Introduce the duplication to your WT nucleotide sequence. Paste the entire nt sequence and highlight the duplicated sequences. Translate. Paste a snip of the translation result. Describe and explain the translation result.
b. Do a Dotmatcher of the nucleotide sequences encoded by the normal allele and the mutant allele. Describe your dot plot pattern.
c. Do a Dotmatcher of the amino acid sequences encoded by the normal allele and the mutant allele. Describe your dot plot pattern. Contrast the pattern with 2b.
d. Perform a global alignment of your normal and mutant proteins. Snip the alignment and scores. What are the % identities, similarities, score?
e. Perform a global alignment of your normal and mutant DNA sequences (alleles). It is possible to have the same observation if there was a sequencing error. Compare and contrast with 2d. Which approach, nucleotide or protein alignment, is better in revealing the possible presence of an indel between the original and the sequence with duplication?