An Introduction to Geneious

On Tuesday, 10/01/2019 at 02:00 PM, we started out dry lab session using Geneious software. I’ve previously downloaded this software during summer to analyze sequences from Prof. Zimmerman’s Lab, so my free trial expired prior to lab session. I had to connect to the¬†operating system on the basement server that is hosting the 2 Geneious floating licenses. Next, I selected the local folder and created a new folder called “Molecular Ecology Fish Barcodes”. After that, ¬†I downloaded the classes DNA barcoding sequences from Canvas. When the folders were downloaded, I dragged and dropped them into my Fish Barcode Folder. I created another file called “Emre Ovet Fish Barcodes and dropped two forward and reverse sequence files there. Then, I assembled the forward and reverse sequence reads of the same sample. I opened those assembly sequences, trimmed the low quality bases and fixed the ambiguities. Next, I generated consensus sequences and blasted them. The top hit for my sequence EO01 was Pseudomonas fragi which is a gram negative bacterium and the second hit was Clarias gabonensis which turns out to be a catfish species. This sample was labeled as Coho Salmon in the supermarket. The top hit for my sequence EO04 was Thunnus albacares which is Ahi Tuna. It was labeled as such in the supermarket. After the Blast results, I’ve builded alignments with my sequences. EO01 didn’t match the species I was supposed to have been served but EO04 did. Moveover, EO01 had a total of 106 polymorphic sites and EO04 had 40.

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