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Bioinformatics Part IV

Updated on June 19, 2013
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The Finale

What other evidence is there that humans and chimpanzees had a common ancestor? Alu sequences are short pieces of repetitive DNA that appear to have inserted into the genome at random. The vast majority of them are found in identical places in the human and chimp genomes, which strongly suggests that they were inserted in the common ancestor of humans and chimpanzees before their lineages diverged.

Today marks the six month anniversary of my first talk given at an American Scientific Affiliation Annual Meeting! In the final post of the series taken from this talk, I will demonstrate how to use Genome Browser (see previous posts in this series) to compare Alu elements from both human and chimpanzee.

Because Alu elements are short pieces of repetitive DNA, they are classified among SINEs (Short Interspersed Elements). Taking an example: AluSq2, an Alu element found within the SPTLC2 gene in humans. The SPTLC2 gene encodes a protein that participates in the synthesis of proteins that play roles in signal transmission and cell recognition, and is conserved in chimps, as well as other primates.

Let's see if this Alu element exists in chimpanzees. In Genome Browser, I've searched the SPTLC2 gene in human. Scroll down to this screen, and expand the RepeatMasker track, which will display both SINEs and LINEs (Long Interspersed Elements).

Mousing over the black bars that are displayed in this track will give the names of the repetitive elements present within the SPTLC2 gene. Clicking on one of them, here I've selected AluSq2, will take you to more information:

Here's the catch...

Now, searching the chromosomal position, displayed as a hyperlink in the above image, in the chimp genome yields an entirely different screen. The Alu element is not present.

So, in fact, not all repeated elements are conserved between humans and chimpanzees. I’ve demonstrated with this example the ability of the database to visually display the dissimilarities between the chimp and human genomes.

A note to say here that this example does not disprove the common ancestry of chimpanzees and humans, but it is a difference worth noting.


The Point

You get the point. In this series, I have shown you how to utilize various internet databases containing primate sequences and annotations to make sense of the common ancestry arguments for yourself. I hope you've enjoyed the series, and found something interesting or useful here!

I've also included a list of bioinformatics databases, most of which we've talked about, that you might like to check out!

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