Behind the story of MEGA7 (and a little guideline)

I have completed my bachelor degree with a major utilization of fisheries and marine resource (PSPK), Fisheries and Marine Faculty (FPIK), much more what I have been learning in mathematics and physics pathway. However, in senior high school, I have identified that I have been interested in the field of biology. I tried to enter Gadjah Mada University (UGM) with biology specialisation. I have tried three times to enter the UGM from all kind of selection process. But, it’s written for me that I have to be in Brawijaya University (UB) with major PSPK. I did not regret because it was really nice and a bunch of things that I can learn. Then, in FPIK I met with a wonderful person with different background, culture, thinking and achieve several achievements as well. Until I finish my bachelor degree, I still fall in love with biology.

Sometimes, I was sneaking out from reality that I was PSPK alumni. I bought many books relate to biology, even though not all of them have been read. Through a long and tiring process, I decided to continue my study to master degree in Wageningen University and Research Center (WUR) with major Aquaculture and Marine Resource Management. However, after I have completed several courses during my master degree, I have not found that the course fits for my interest. I like it but I did not really into it. Still, I found myself, enjoyed reading essential ecology and biology (Campbell), it was calling me about how to be a student who joins Biology Olympiad at school. I recorded myself in front of a camera and talked to myself. Why I did not get what I like and I am still doing it? Then, I realized a sentence from my teacher “it’s written” and I have to thank God for it. Because I never know what is the story behind it and it’s 100% true. I can learn anything from anywhere not only in the class but overseas. I would like to share to you about my little experience to using MEGA7.

MEGA is an abbreviation of Molecular Evolutionary Genetic Analysis, free download software on the website, created developed by Koichiro Tamura, Glen Stecher and Sudhir Kumar (1993-2016). The latest version was launched in 2016. MEGA is well-known for geneticist or whosoever learn molecular genetic and/or bioinformatic. MEGA version 7 is a program to edit Deoxyribonucleic acid (DNA) to identify what kind of species that we have based on our sequence data. Several steps below:

  1. Open MEGA 7 and click on alignment – edit/view 1
  2. Open the file from your sequencing result (one of the filetypes is AB1)
  3. You have a forward and reverse data. First, you can start with forward data (select the data which not clear enough which paired base (A T G C) belongs to which line and you can delete them (e.g., picture below)
  4. 2Then, you can click on “Add unmasked sequence…” (picture below)
  5. 3Afterward, you get other appearance (like picture)4
  6. You will do the same steps (3-5) in the reverse file. The only different is you have to click on “Reverse complement sequence” before you delete/edit your DNA code.
  7. Then, you will have a paired of your DNA code (forward and reverse) 5
  8. As following, you have to block all the DNA code (control A) then click on “align selected block by ClustaIW” – align DNA – OK6
  9. If you have a good result, it shows like this (picture below)
    7you can clearly see that if the (*) sign which mean that your code is good and if between (*) there is an empty space (no code) you can copy and paste your code to the original file to compare what is the real data about.
  10. Finally, you can save your data by click “file-export alignment- FASTA format. Then you can open your saved file (open with-notepad-copy-paste into NCBI website – and click BLAST – you get your species)8

Special thank to: Mba Nani atas ilmunya 🙂

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