10/3/18 Wednesday. Today, I used Geneious to look at my forward and reverse reads, however my reads weren’t successful so I had to used the given three forward and reverse reads which are CO-01-Albacore, CO-02-Big eye tuna and CO-03-Yellowtail.

I received “An Introduction to Geneious” handout with instructions on how to use Geneious and do the exercises. I first downloaded all the forward and reverse reads and drop the file into the folder that I named “Jinwoo Kim DNA barcoding for Molecular Ecology”. Next, I looked both forward and reverse reads to see how good they were and the HQ% was around 90s so they were very clean. Using CO-01, I tried looking at the sequence by clicking sequence view and also tried editing the nucleotide bases and etc… but never saved it. After that I copied the reverse sequences CO-01 into the forward reads folder. I then selected both of them and right clicked to choose ‘De novo assembly’ to assemble the two reads. Next, I clicked the created file named ‘assembly’ and zoom in to see the overlap of reverse and forward reads. Mine had high HQ% values so I was able to cut the ends of both sequences and was good to go. After the trimming the mess, I saved the file and choose ‘Generate consensus sequence’ and clicked ok. I BLAST the assembly ‘consensus sequence’ and resulted to have scientific name of the organism that has the highest matching sequence to mine. I searched up the scientific name to see if its the correct fish. At last, I copy and paste 5-7 alignment to my created folder named “Fish barcode test alignment’ and selected them all to click ‘Multiple align’ and get a new ‘nucleotide alignment file’. I followed this steps for CO-02 and 03.

Exercises:

1. CO-01—– Matched, Albacore=T.alalunga,  CO-02—–Matched, Big eye tuna=Thunnus albacores, CO-03—–Matched, Yellowtail=Seriola quin queradiata.
2. CTTTTCTGATG (first 10) and total of 18.