October+2012

toc Goal for the month
My goal for this month is to learn more about bioinformatics and download some useful already created GUI's and apply my knowledge of both bio and MATLAB to get a better handle on what I learned last year. I am hoping that I can understand how the GUI works both from a programmer perspective; that way I can alter things to use them as I wish and also from a user perspective; being able to use them to their fullest abilities and continue on in my research.

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Quick review of GFP from last year. It went over how GFP is used at a genetic tag and has helped be able to track things such as the progression of cancer sells and the proliferation rate of other cells. Research using GFP was awarded the Chemistry Nobel Prize in 2008.

I began by looking at a MATLAB video that embraces the bioinformatics tools that are already in the toolbox for MATLAB. First I went into ncbi and looked in the nucleotide database for DNA of a zebrafish which is Danio rerio. I used the seqtool and copied the locus from ncbi (national center for biotechnology information) and entered the code:

>> S=getgenbank('NM_131509'); >> seqtool(S)

getgenbank is a command saved into MATLAB for this tool and lets you access the online data base of ncbi to pull out it genetic coding without having to do it yourself. After entering the above code into MATLAB, the sequence tool came up with this:









the sequence is shown and you can explore each of the different settings once you have the genetic coding. I can look at the complete sequence or its reversed complement which is used for tagging the DNA during PCR and is helpful in reconnecting the vector. Last year I created a pGLO code which this would have been helpful for. And it shows you the comments and data from ncbi which is very helpful.

Notes/Findings
CDS- coding sequence

ganglion cells create the optic nerve

all light is focused to the fovea or focal point in the back of the eye. The lens of the eye is convex so the light converges at the fovea for objects in our direct vision. Objects in our peripheral vision do not come into focus because the light is being reflected to another part of the retina which has less cones than the fovea which causes less detail to be apparent which is why we can notice things in our peripheral vision but cannot experience all the details.

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Francis Raycroft recently sent me the above link which explained what CDS, complement sequence and reverse sequences are. It gave an example of a sequence and pointed out which bps would be used for the PCR primer which I learned and did last year. It also talked about the standard method of how primers are named, 5' to 3' is the standard method. And that reverse sequences bind opposite the separated DNA strand. It binds 3' to 5' and is the complement to single helix DNA strand. The complement sequence runs the entire length of the sequence where the reverse and sequence primers only run along the bps needed.

The sequence shows from 15919 to 16569 bps and the purple highlighted begins the reference strand binding 5' to 3' along the complement strand. The top strand is one part of the helix and the bottom strand is its complement which you can see starts at 3' to continue binding to the first base pair. Then the greenish colored highlight begins binding at 16400 bps toward 15972 and the dark blue begins binding at 16520 to 15972 going 5' to 3' along the original strand as opposed to the complement strand. And the dark green and blue are primer pairs and would be used during PCR to duplicate the DNA. It would bind to that section and multiple.

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The video above from YouTube went over PCR from last year. I reviewed the concept of PCR and the steps; especially the amplification of target DNA using PCR. We use it to replicate millions of our target sequence to use. This is very helpful because it can be done without purification.

New MATLAB
I began exploring the new updated version of MATLAB which is much different than the old version. Everything is laid out very differently and there are now apps that you can interact with and a new plots tab. Also the play button has disappeared and is now called 'Run and Time' and the editor cannot be docked and is brought up by summoning "New Script". The 2012 version has many more features than 2011 but is a little more complicated in running when used to the old matlab. The editor not being docked is a large difference which makes window switching happen more often.



I began looking at the sequencer on the new version of MATLAB and figuring out where the code can be entered to reach the ncbi database for nucleotides. I just entered it into the command window but I'm sure that the script can be entered into the editor and work.



What is Sequencing Analysis?
[|Wiki Answer]

Sequence Analysis allows us to look at the specific makeup of a piece of DNA and running it through different databases and alignments in order to compare and contrast the DNA to other pieces of DNA in order to analysis and find similarities. On NCBI, you can blast a nucleotide sequence and find similar sequences that either match 100% or what percent of the sequence matches. The tool in MATLAB is similar and takes each part of the sequence using the locus and breaking it down that way.

[[image:descro[topm_.png width="800" height="576" caption="a description on my blast of a nucleotide of Danio Rerio"]]

Off the beaten path
I attempted writing a MATLAB code for my chemistry problems involving solving for simple variables. As that works on MATLAB and I successfully wrote that code, I could not transfer it to a GUI to be able to use on my mac book In order to use this type of equation in a GUI, I need to learn more about how a slider bar would work because the callback functions function similarly. The code was simple, getting the program to display the speed of light and saving that as a variable as wavelength when solving for frequency and same for when solving for wavelength, the user just plugs in their given frequency. Another problem is conversion; MATLAB does not include the units of each variable so converting would need to be done before using my program, I need to take into effect conversions next.

Month in Review
For this past month, I explored the bioinformatics side of MATLAB and studied and will continue to study what I can do with MATLAB in terms of my biology background. I dug deepest into the sequencer tool of MATLAB. I understand the concept of how the program pulls up the locus number from the NCBI website which is the site it is programmed to take from. A programmer could easily change the database in which the program pulls from, but the NCBI website is so widely used that it would make very little sense to change it. I looked at a few different sequences I learned and experimented with last year. I looked at Danio Rerio which is the Zebra fish and also the pGLO of GFP which is what I studied Fall 2011. The tool will tell you the percentage of each nucleotide and allows you to easily access the reverse sequence.

I also began studying what the importance of sequence analysis is and what it is used for. Sequence analysis is important in the study of DNA and other complementary strands.