Genomics data analysis
Data Dive 5 Gene Alignment Why are we doing this? We know that gene structure and function can change over time. These methods help us visualize and understand those changes. ————————–Part 1: There are many histone regulatory proteins identified in Drosophila. Let’s look at a few. 1. Go to the UCSC Genome browser and search for “histone deacetylase” in any species. To facilitate our ability to do this asynchronously, I’ve collected several of three yeast sequences here: Data Dive 5 – HDAc Sequences 2. Go to the EMBL database of tools: https://www.ebi.ac.uk/services/data-resources-andtools a. Check the box for “DNA & RNA” b. Choose Clustal Omega c. Paste in your FASTA sequences (make sure you’ve selected “DNA”) and submit. While the program is running, read about how Clustal omega works. d. When the results come up, look at the alignment under “Tool output”. This will show you the nucleotide alignment. You should see some regions that align poorly and some that align well. e. You can also look at the “phylogenetic tree”. Q1: Make some observations about the results. If you’re having trouble, I ran this analysis on 4/7. The results will be available for 7 days. DHL’s Clustal Analysis 3. When I look at similar data, there is a conserved region across all the HDAcs. Presumably, all HDAcs have an protein-binding domain and deacetylase enzyme domain. From humans to yeast, there are several classes of HDAc. Let’s align the fly versions with versions from yeast. a. Look in the UCSC Genome Browser at the structure of Drosophila HDAC6 and HDAC11. b. Here is a file that includes both the yeast and drosophila genes: Data Dive 5 HDAc Sequences with drosophila c. Run a CLUSTAL analysis and see if you can tell which type of HDAc they are. Q2: What is the difference in these HDAc proteins and which type are the Drosophila proteins you looked at? What does that tell us about the HDAc proteins in drosophila. 4. Our analyses so far help us understand gene function, but not gene evolution. Let’s try to find HDAcs from across various taxa and see how they’ve changed over time. As always, proteins are named in the order they were discovered in each species. So HDAC1 in one species might be most similar to HDAC7 in another species. Let’s pick 1 and find it’s closest homologs first. a. Go to https://www.ncbi.nlm.nih.gov/gene b. Search for histone deacetylase c. Pick one of the results that seems real and click on it to get to the DNA sequence. You will need to look through the results until you find the “NCBI Reference Sequence” section. Click “FASTA” to get the mRNA sequence in FASTA format. i. ** Take care to get the GENE sequence and not the GENOME sequence”. Ask me how I know. Lol. ii. Also, make note of whether you have the RNA sequence or the protein sequence. Use this to decide which type of BLAST to use. d. Blast the DNA sequence. 5. The BLAST results appear in a few formats. Click a couple to see what’s available. a. Then, look at “other reports” and choose “MSA Viewer” to see the multiple sequence alignment data. b. Go back to “other reports” and choose “Distance Tree viewer”. Q3: What are the nearest sequences to the one you chose? What does this tell us about the evolution of this gene? Q4: If you wanted to learn more about this gene’s evolution or function, what would you do next?
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