describing the methods you used to identify the homologs.
Read the instructions carefully and to the very end or you WILL lose points.
A. Using the accession number of the protein assigned to you for the term project, identify the best match for this protein in the following organisms (exclude the organism your sequence belongs to) and assess if you consider it a putative homolog:
Yeast (Saccharomyces cerevisiae)
Slime mold (Dictyostelium discoideum)
Tetrahymena thermophila
Thale or mouse-ear cress (Arabidopsis thaliana)
Nematode worm (Caenorhabditis elegans)
Fruit fly (Drosophila melanogaster)
Western clawed frog (Xenopus tropicalis)
Zebrafish (Danio rerio)
Mouse (Mus musculus)
Human (Homo sapiens)
Note:
1. You can use multiple methods, algorithms, and databases for a comprehensive search ( e.g. BLAST, SmartBLAST, Psi-Blast, Delta- Blast, Homologene, Uniprot, keyword search, optimal alignment algorithms, etc)
2. Protein names/titles are often misleading – base your putative homolog on actual similarity in the sequence and domain architecture
3. You may have to change the algorithm parameters to get results if the sequences you are looking for are quite divergent from your sequence
4. It is possible you may not get any hit that fits the criteria of a putative homolog in a particular organism or multiple accession numbers that fit the criteria.
Document your results for each organism by providing the following for the best sequence match(es) that you identified:
1. Accession number
2. FASTA sequence
3. CDD Domain Architecture
4. Alignment with % identity and similarity, %Query Coverage, and E-Value
5. Brief description of what strategy was used to identify the best match
6. Discussion of why or why not this should be considered a putative homolog for your sequence
Important: DO NOT cut and paste randomly or provide screenshots of entire pages of BLAST results etc
B. Write a draft methods section describing the methods you used to identify the homologs. (A published paper from my lab is provided as an example for writing methods for computational analysis).
Note: This is different from point 5. in the above section. This is a single paragraph describing methods for the entire exercise in a formal scientific writing style.
Lastly, don’t forget to cite your sources including databases, algorithms, etc. Use the published paper on the algorithm
A Sample assignment is provided from the previous semester’s assignments. You DO NOT have to format it exactly like it, it is just to give you an idea. Use your own style and formatting to best convey the results. DO NOT plagiarize from the student sample – it is only there as a guide.