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Getting Started in Desktop Bioinformatics

Thursday, July 25, 2013

I've spent about four months now exploring do-it-yourself desktop bioinformatics. Overall, I'm excited by what I've been able to do and I'm optimistic about the prospects for other do-it-yourself desktop-science geeks, because there are tons of great online tools for doing bio-sci and lots of important scientific questions yet to be fleshed out. So I thought I'd share some of what I've learned, and provide some pointers for anyone who might want to try his or her hand at this sort of "citizen science."

It helps to have the benefit of a science education (in particular, a bio education) before beginning, but one of the great things about do-it-yourself desktop science is that you can (and will!) learn as you go. For example, you might have only a bare-bones basic understanding of enzymology before you begin, but as you move deeper into a particular research quest, you'll find yourself wanting to learn more about this or that aspect of an enzyme. So you'll hit Google Scholar and bring yourself up-to-date on this or that detail of a particular subject. That's a Good Thing.

When I first plunged into DNA analysis, I have to admit my knowledge of mitochondria was weak. I knew they had their own DNA, for example, but it wasn't obvious to me (until I started digging) that mitochondrial DNA is pathetically small, whereas the mitochondrial proteome (the superset of all products that go into making up a functioning mitochondrion) is large. In other words, most "mitochondrial genes" are not in mtDNA. They're in nuclear DNA. There are a couple of online databases of nuclear mitochondrial genes (NUMTs, as they're known), but by and large this is an area in dire need of more research. Someone needs to put together a database or reference set of yeast NUMTs, for example. We also need a database for algal NUMTs, another for protozoan NUMTs, another for rice or corn or Arabidopsis NUMTs, etc. Maybe you'll be the one to move such a project along?

So. How can you get started in desktop bioinformatics? I recommend familiarizing yourself with the great tools at genomevolution.org, which is powered by iPlant, which (in turn) is funded by the National Science Foundation Plant Cyberinfrastructure Program here in the U.S. In particular, I recommend you set aside an evening to run through some of the tutorials at genomevolution.org. That'll give you an idea of what's possible with their tools.
Many organisms have genes for flagellum proteins,
but not all such organisms actually make a flagellum.
(The flagellum is the whiplike appendage that gives the
cell motility. Above: Bdellovibrio, a bacterium with a
powerful flagellum.)

If you go to this page and scroll down, you'll find some really interesting short videos showing how to use some of the genomevolution.org tools. They're fun to watch and should stimulate your imagination.

What kinds of problems need investigating by desktop biologists? The sky's the limit. One quest that lends itself to citizen science is looking for examples of horizontal gene transfer (HGT). This requires that you first teach yourself a little bit about BLAST searches. (BLAST searches are sequence-similarity searches that let you compare DNA against DNA or amino-acid sequence against amino-acid sequence.) The strategies involved here can range from simple and brute force to sophisticated; and the great thing is, you can invent your own heuristics. It's a wide-open area. I recently found good evidence (90%+ similarity of DNA sequences) for bacterial gene transfer into rice, which I'll write about in a later post. I'm confident there are thousands of examples of horizontal gene transfer (whether from bacteria to bacteria, bacteria to plant, bacteria to insect, or whatever) waiting to be discovered. You could easily be the next discoverer of one of these gene transfers.

Here are some other ideas for desktop-science explorations:
  • Find and characterize flagellar genes in organisms that lack motility. If you dig into the literature, you'll find that there are many examples of supposedly immotile organisms (like the intracellular parasite Buchnera, which lives inside aphids) that not only harbor flagellum genes but express some of them—yet have no external flagellum. Obviously, organisms that retain flagellum genes but actually don't make a flagellum (that little whip-like tail that makes single-celled organisms swim around) must be retaining those genes for a reason. The gene products must be doing something. But what? Also: Paramecium and diatoms and other eukaryotes make flagella and/or cilia. Most animals also make cilia. (Ever get a tickle deep in your throat or bronchia? It was probably something tangling with the cilia lining your bronchial system.) What's the relationship between cilia gene products in Paramecium, say, and cilia in animals? Do any plants conceal cilia genes? If so, how are they related phylogenetically to lower-organism cilia?
  • Migration of genes from parasites to host DNA. A general pattern that seems to happen in nature is: a bacterium or other invader takes up residency inside an animal or plant cell, becoming an endosymbiont; then some of its genes (the symbiont's genes) move to the nucleus of the host cell. Which genes? What do the genes do? That's up to you to try to find out. 
  • Bidirectionally ("bidi") transcribed genes: While rare, there are examples of genes in which each strand of DNA is transcribed into mRNA. (The genome for Rothia mucilaginosa contains many putative examples of this.) Find organisms that contain bidi genes. Try to determine if both strands are actually transcribed. Examine sister-species organisms to see if one strand is transcribed in one organism and the other gene (on the other strand) is transcribed in the other organism.
  • Phylogenetics of plasmid and viral genes. Try to determine the ancestry of a virus gene. There are good tree-making services online that do all the hard work for you, including protein-sequence alignments. All you have to do is cut and paste Fasta files.
  • Codon analysis. There are many plants (rice is one) and higher organisms in which DNA is more or less equally divided into high-GC-content genes and low-GC-content genes. Surely the codon usage patterns for each class of gene(s) varies. But how? What are the codon adaptation indexes (CAI values) for the various genes? Create a few histograms of CAI values. Use CAIs and other techniques to try to determine which genes are highly expressed. Are HEGs (highly expressed genes) mostly high-GC? Low-GC? Both? Run some histograms on the genes' purine (A+G) content, G+C content, G+C content by codon position.
  • Many organisms (and organelles) have extremely GC-poor genomes. Some have bizarre codon usage patterns (where, say, the codon AAA is used 12 times more than the average codon). Some use 56 or fewer codons (out of 64 possible). Find the organelle or organism that uses the fewest codons. See if there's an organism or organelle that uses fewer than 20 amino acids. Which amino acid(s) get(s) left out? 
  • Characterize the DNA repairosome of an aerobic and an anerobic archeon. Compare and contrast the two.
  • Find all the genes in a particular organism that have mitochondrial-targeting presequences in their DNA. 
  • Pick two closely related organisms. Try to figure out how many million years ago they diverged. Use mitochondrial DNA analysis as well as cytoplasmic protein analysis. 
  • Find the bacterium that has more secretion-protein, permease, and protein-translocation genes than any other. Compare it to its closest relative. 
  • Find an organism that is pathogenic (to humans, animals, or plants). Find its closest non-pathogenic relative. Compare genomes. Determine which genes are most likely to be involved in virulence. 
  • Some seemingly simple organisms (amoebae) have more DNA than a human. Why? What's all that DNA doing there? Does it contain horizontally transferred genes from plants, bacteria, archeons, animals? Are amoebas and other super-large-genome organisms "DNA hoarders"? Are they DNA curationists? Characterize the genes (enumerate by category, first) of these organisms. How many are expressed? How many are junk? What's the energy cost of maintaining that much junk DNA? Can it all be junk? Is an amoeba actually a devolved higher life form that forgot how to do morphogenesis and can no longer develop into a tadpole or whatever?
  • [ insert your own project here! ]

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