EMATM0004 - Computational Genomics and Bioinformatics Algorithms - Report Writing Assessment Answer

Assessment Task:

EMATM0004: Computational Genomics and Bioinformatics Algorithms Report Writing Assessment Answer

TASKS:

1) Report the full taxonomic name (from Taxonomy Browser) of the species under investigation, and the accession number of the complete mitochondrial DNA sequence (mtDNA) of one of them. Retrieve the sequence. Report basic statistical descriptions of the data and discuss its main features (use Matlab demos and earlier labworks for ideas and code). Find protein-coding genes, and translate 2 of them (including CYTB, the other one is free, you could use CYTC). [cytochrome B and cytochrome C]. [if
you are working with a species that does not have a full mtDNA in genbank, answer task 1 by using a related species]

2) BLAST the translated version of CYTB, and report (at least) the top 5 matches: what organisms are these? Discuss the results. [use protein blast]. If the top 5 matches are in the same species, or in very close species, you can also choose species that are lower in the blast ranking. The idea is to end up with a group
of 5 or 6 related species, for question 3.

3) Generate a rooted phylogenetic tree for the species above. Discuss the evolutionary history of your chosen organism or group (major branching events and their order) based on these sequences. use an outgroup.

4) Add any other species whose relation to the organism you want to study. In this case you can reduce the set of 5 closest matches a little, if you have added some extra species you want to investigate. This set of species includes all those that you are studying, as well as some of the closest neighbors of then sequence we started with. For each species, locate CYTB and CYTC (or another mtDNA protein you have chosen to use instead of CYTC), and compute the genetic distance between each pair, separately for each type of protein-coding sequence. Justify your choices.

5) Generate rooted phylogenetic trees for CYTB and CYTC (or the protein you chose to work with), by using an outgroup. Are they different? Can you generate a consensus tree? Repeat the process above (for the same 2 proteins) to have one comparison at the DNA sequence level, and one at the amino acid (AA) level. Compare the resulting trees (4 trees should result from this study: CYTB AA, CYTB NT, CYTC AA, CYTC NT).

6) Discuss the phylogenetic relations between the species you are investigating, found in the tree that you generated. How does your tree compare to that found in Taxbrowser? This part is deliberately open ended, as it will depend on the kind of question you are trying to answer. How do the species of interest relate to each other?

7) Perform multiple alignments for both proteins, and discuss polymorphic sites in the 2 proteins under investigation.

8) Make use of some article from Pubmed that discusses related questions. How do your findings relate to that article? Have you found an article that agrees/disagrees with your findings? Are the methods different? Are the results comparable? Do you see any limitations in the methods that you have used?

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