Bioinformatics Week 1 'Work Products'

Please note that all items turned in should be properly formatted. For example, sequence information must be properly aligned to be readable. This may involve converting to a 'mono-spaced' font such as Courier, changing the font size and/or the margins of the document to eliminate disrupting line breaks. Check that your materials are attractive and interpretable as submitted.
  1. Manual translation (photo of paper translation) - be sure to translate all codons, identify stop codons and the ORF.
  2. Your DNA Pol I / polA gene nucleotide sequence in FASTA format. [Exercise 2]
  3. Translated sequence in 'with nucleotide seq' format - only the correct reading frame, with highlighted stop and start codons. [Exercise 3]
  4. Human protein-of-interest sequence variant analysis. [Exercise 4 - see details within that section, but includes the variants analysis based on AA type alone (4A) and the MSA with your analysis based on AA conservation within the protein of interet (4B).]

    4A. i. What is the type of AA (original) vs. the variant?
    ii. What is the score (using the BLOSUM62 substitution matrix) for the change?
    iii. From this information, do you think this AA change is a minimal, moderate, or radical change?

    4B. i. MSA with AA variant locations marked. (Include a copy of the FASTA file used to create the MSA, and a key to the species used in your alignment in your ELN.)
    ii. Analysis of variants based on location in the protein and conservation.

  5. Screenshots of protein-of-interest from exercise 4 viewed in iCN3D, showing AA sequence window with AA selected and AA visible in the protein structure, for each of the variants you analyzed. [Exercise 5]