Bioinformatics '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. Exercise 1 - Manual translation (legible photo of paper translation) - be sure to translate all codons, identify stop codons and the ORF.
  2. Exercise 2 - Your DNA Pol I / polA gene nucleotide sequence in FASTA format.
  3. Exercise 3 - Translated sequence in 'with nucleotide seq' format - only the correct reading frame, with highlighted stop and start codons. [Exercise 3]
  4. Exercise 4 - Human protein-of-interest variant analysis - multipart section (see details within that section)

    Preparation for Variant Analysis

    A. Your POI AA sequence with variant locations marked.

    B. MSA with AA variant locations marked. (Include a copy of the FASTA file with multiple AA sequences that you used to create the MSA, and a key to the species used in your alignment in your ELN.)

    Variant Analysis

    C. Variant analysis based on AA type change only.
    i. AA type change (original vs. the variant)?
    ii. BLOSUM score for the change (using the BLOSUM62 substitution matrix)?
    iii. Summary: From this information, do you think this AA change is a minimal, moderate, or radical change?

    D. Variant analysis including MSA information on location in the protein and conservation.

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