average gene length in prokaryotes (part 1)

One of my side research projects involves processing large numbers of genomes (specifically, all fully-sequenced prokaryotic genomes). Since I’m playing with the data anyway, sometimes I end up with random questions that can be answered with what I already have on hand. One such question is this: “What is the average length of a prokaryotic gene?” We could figure this out fairly directly, but it’s always best to have a prediction in hand first. After all, if we have no idea what kind of values to expect, how can we trust the accuracy of a more direct (and experimental) method?

So what do we know? There are 4 possible bases (A, G, C, and T) and three such bases make up a codon. This means that each position of the codon can be any of 4 bases, so there are 4*4*4 = 64 possible codons. Of these, 3 are stop codons (meaning that they mark the end of a gene). We generally think of there being only 1 start codon (ATG, coding for methionine), but it turns out that prokaryotes often use other codons instead. Plus, if there are multiple ATG’s in the same stretch of DNA, how do we know which is the actual start?

For example, take the sequence:


This sequence has two potential start sites (in bold) and two stop codons (in bold italics). We can unambiguously choose the first stop codon, but we have no way of knowing without more evidence which start codon is the real one.

To get around this, let’s take a conservative approach in calling sequences a “gene”. Instead of anything beginning with a start codon and ending with a stop, let’s take the entire genome and blast it to bits by cutting at every stop codon.

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Comp Bio is complicated

I finished up my first lab rotation two Fridays ago, here at UT Southwestern. It was a pleasant few months with an interesting project, consisting mostly of starting at a computer screen and writing Python scripts, running BLAST searches, and so on. To summarize, but leaving things vague (both for most-people-don’t-care reasons and the-data-is-unpublished reasons), the project was this:

There are currently a crap-ton (“crap-ton” is a standard scientific prefix) of bacterial and archaeal genomes published and available on NCBI‘s servers. Archaea, like bacteria, are single-celled prokaryotic organisms. However, they differ from bacteria genomically (and therefore metabolically) in many ways. Some archaeal properties are like those in eukaryotes (like us!), while others are like those in bacteria. So one of the huge unanswered questions in evolution is: how are bacteria, archaea, and eukaryotes related to each other? Or, how would we make a tree of life relating these three domains?

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