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Lab 6: An Introduction to Geneious

October 1, 2019


We began our lab session by downloading a software called Geneious. Geneious is a commercial program that performs many functions on DNA and protein sequence data. I first created a folder where I was able to download and store Fish DNA barcoding sequences from canvas. The folder contained both the reverse and forward reads and contained the chromatograms of our sequences. However, when I clicked on the forward read of my sequence it looks like I did not have a very successful PCR run at all. This may mean that bacteria or fungi could have contaminated my sample or that my sequencing run was a complete fail. Because of this, I used the sample sequences from other students which were much more successful in their PCR runs. I used the files “ARA01” and “BP01” as my new sequences. After I dropped these files into my “Fish Barcode” folder, I was able to begin assembling the forward and reverse sequences of the sample “BP01”. In this step, I was able to examine my sequences and delete any bases on the two ends that were unreadable or trim off any ambiguities. Once that was completed, I generated a consensus sequence and put it into a new file where it was ready to undergo BLAST. BLAST stands for Basic Local Alignment Search Tool and is used to search the database for highly similar sequences. The top hit for my sequence BP01 was Thunnus obesus which is yellowfin tuna. This is exactly the name of the fish that the student was told when they purchased it. For the sequence ARA03, I found that the top hit was Seriola quinqueradiata which is Yellowtail or Japanese amberjack. Once again, this is exactly the name of the fish that the student was told when they purchased it. There were polymorphisms present in both of these sequences. In the ARA03 sequence, I found 599 polymorphisms which were all SNPs. The first 10 polymorphisms were at sites 63, 68, 70, 89, 92, 95,113,128, 131, and 146. In the BP01 sequence, I found 8 polymorphisms which were also all SNPs. The polymorphisms were at sites 9, 275, 291, 363, 384, 405, and 418.

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