Bioinformatics 'Work Products'

Please note that all items turned in should be properly formatted. For example, sequence information should 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 (paper) - 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 with your MSA. [Exercise 4 - see details for this part at the bottom of that section.]
  5. Screenshot of protein-of-interest viewed in iCN3D, showing AA sequence window with AA selected. [Exercise 5]
  6. Processed FGENESH analysis of your genomic sequence, including information from both Exercises 6 and 7.

    Create a simple table of your results, titled and with any appropriate notes below:

    FGENESH analysis results for Omy_Node15a.seq (O. myriophila genomic DNA) - Predicted Genes
    Gene density: average 1 gene / 5400 bp DNA
    Gene strand No. of exons Protein length (AAs) BLASTP match? BLASTX match?
    1 + 9 379 yes yes
    2 + 13 465 yes yes
    3 - 3 123 yes yes
    4 + 6 798 yes yes
    5 - 1 37 no no
    6 etc.        
    * - 2 45? not done yes

    *Notes: One possible gene found by BLASTX not detected by FGENESH, between genes 4 & 5.