Geneious – Let’s decode some DNA

June 13, 2009 at 8:27 pm (Chemical engineering) (, , , , , , , , )

This article is about a bio-informatics program which is capable of manipulating data gained on genetics. It’s important to notice that this program is not free… But the basic edition of this is free (and doesn’t time up) and runs on Linux.

The big long tough end semester exam of my chemical engineering (includes biochemical engineering) degree is now over. So, I can blog again friends… I thought of giving a start from stuff currently on my head!I found this brilliant program some time ago Gene – eious , name implies it’s work…..truly this is a work of a genius! It was a quiet a bit of surprise to me as I didn’t think that bio-informatics has come this far.

The code of virus HIV, good heavens!  (version 4.5.4 running on FC9)

The code of virus HIV, good heavens! (version 4.5.4 running on FC9)

Usually people need to take help from many programs like blast, pymol, swisspdb viewer to view and manipulate coding in DNA, proteins, nucleotides,virus and other stuff. Simply it has been a mess. Blast is a powerful pattern matching search engine for sequences of codes (genes), but it lacks the help of a good GUI to to show it’s results.

And you have to manually search and download genetic codes without this kind of program ….. You may think it’s nothing …. I’m talking about a one of the biggest databases in the world… the human genome alone won’t fit on to a DVD ! Features of this doesn’t stop here.

Graphics used in presentation of data in Geneious is excellent, one of the best Java GUI I had seen. It’s very user friendly.

The shape of DNA in 3D -- you rotate or edit.

The shape of DNA in 3D -- you rotate or edit.

If you don’t understand a thing I say, let’s go and have some fun. When you open up the program there’s a sample documents folder on tab on the left. Click any of these to load the default files available. You can watch the code of the virus HIV, the code of a mice gene, and some human gene too… Isn’t it awesome? These tiny little scary things?

Comparison of animals by sequence of code

Comparison of animals by sequence of code

The features of Geneious is too big to mention here… You can go to the about page on their website for a list of them. Or you can download the manual in PDF format here.

Computer geeks may think what is the relationship bio-stuff with codings… decode DNA? (like in computer programs– but they are machines?) . I have mentioned why in a little note at the bottom of this article. Just scroll down.

Installing Geneious:

Simply visit their download page at this link.  If it’s linux, you’ll be downloading a .sh file. You can double click on this file after download to install. Or type,

./filename.sh as root in command-line

It has a completely inter active installation process like in windows. So installing won’t be a problem. I’m using the version 4.5.3, and the current version is 4.6.4

Sequence of coding of an enzyme (a complex protein)

Sequence of coding of an enzyme (catalyst protein)

The coding of nature (most of stuff is omitted to simplify world for computer geeks ).

Every living thing on earth carries DNA on their cells, which is a encrypted database of all the stuff you need to build a copy of that living being. The whole thing is encrypted as bases Adenin(A), Guanine(G), Cytosine(C) & Thyomine(T). (Similarly in computers, they use 1,0). These are in a sequence like in binary file of a computer (–ATGAGGTAA– in DNA, –100110101– in computers). When decoding, 3 of these in sequence (similar to 8-bit byte) is taken and it gives 4*4*4=64 combinations. But as only 20 amino acids are there, according to the value an amino acid is formed in the other side choosing from that 20 acids possible. As I told you, the DNA is in sequence, so a sequence of amino acids are formed (like a binary 8-bit file). This is cold a protein. The encrypted sequence of code in DNA for building up this protein is called a gene. There are lacks of genes in a DNA (similar to file database in IT).

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2 Comments

  1. Chandima said,

    Hi Malshan,

    I was just happend to visit your blog while googling for ‘mahasona’ virus.

    Amazed to see your posts and the disciplines you currently have embarked in your education plus your achievements. So proud of you, being a Sri Lankan.

    Though i come from MS arena, i do like Open Source stuff very much and YES indeed.

    Anyways, you have done a remarkable job in your blog. Keep it up!

    I wish you all the very best in your studies, family and career.

    Regards
    Chandima

    • Malshan Peiris said,

      Thanks pal …. first time some one praised me this much 🙂 Thanks again.
      Doing both chemical engineering and BIT has it’s advantages, I would say. They cover many science-related fields.
      Although I wrote a review in my blog I think you noticed that I did not made this program. 🙂 And the program “Geneious” is not open source, but free.
      Haven’t put an article for months. Gonna put something this week.
      Have a nice day.

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