I read pretty much the same thing you did*. The various methods of sequencing DNA each have their flaws and advantages. These problems are usually overcome by massively resequencing the same bits (70x times per small sequence isn't unheard of)...however, the same error can occur 70 times. Genomes can have weak spots (for a lack of a better work) that will always break, etc.
In the article, they did the original sequencing using what's called Next-Gen Sequencing/pyrosequencing/454 (which, if they stick with 'Next-Gen', will quickly run into the same naming issues that the video game industry did) - http://en.wikipedia.org/wiki/Pyrosequencing The wiki link has a decent amount of marketing spew in it, btw.
This method is fast and cheap and gives you tiny chunks of data, but TONS of it.
Then they switched to Sanger sequencing, which is slower and more expensive, gives you less coverage, but longer reads (~700 DNA letters). So, they used two systems, each with unique flaws, to verify what was a real mutation and what wasn't.
Sanger Sequencing: http://en.wikipedia.org/wiki/DNA_sequencing#Chain-termination_methods
*There are what's called Cell Lines, however. But I didn't get that they were using any from the article.
Some of these cell lines are officially immortal and, once from humans, are now their own species...
Ahhh! Don't talk about my research proposal.
You're right, of course, everything you said I pretty much hinted at, however. I wasn't wanting to go too in debt (my mistake).
"The coat proteins do more than just carry the DNA to your cells, they allow the virus to actually get inside the cell." == "The outer coating (proteins) are just the vessel to carry the DNA into your cells"
The protein coat, quite often, mimics a molecule that triggers a cell to eat the virus. Granted, that's just one of the methods various virii (viruses?) use.
"There are also more proteins inside many viruses that are essential HIV has several for example." == "Some, however, come with their own spiffy enzymes that embed DNA into your genome so you can make plenty more..."
This being the exact mechanism that HIV embeds itself into a genome. I'm sure you know that an enzyme is a protein (although, technically a RNA enzyme is not a protein...)
I was poorly arguing that it's the data that one has to be worried about in this case. Free-floating DNA can make its way into a cell, it's rare, but it can happen ("the hard part - but can happen easily sometimes"). I should have been a proper biologist and clarified we're talking eukaryotic cells, bacteria pick up random DNA all the time and do it gleefully (note: bacteria do not contain glee). Bacteria then can run the DNA, eat the DNA, whatever it wants to do.
Once there, the data/DNA then creates havoc by existing, the cell's machinery follows the destructive data and starts to build until it dies (doesn't always die). It builds proteins, which are used to build more virii (viruses?) duplicates more DNA/RNA, the virus self-assembles, leaves and continues on with a nice and shiny protein-coat (or whatever it wants to coat itself with, sometimes parts of you).
Much like a computer virus (DNA) embedded in a program (cell). Normal program instructions are ran, the CPU comes across viral opcodes - runs those too - then continues on like nothing happened...assuming it's a well written computer virus. All the business about transferring a virus via flashdisk, floppy, email, etc (protein coat) - while essential - is secondary to the viral payload itself, the code/data/dna/rna. In my opinion...
Bioinformatics is no actual work with chemicals or lab, it's almost 100% computers and stats.
Some people are programming along the lines of what you ask, however, there is even a fancy UI that you click and tell a machine what type of what-have-you pathway you want and *spoot* out comes a bacteria that does what you want.
Very close to being out and about in the world...the link below is a tad old, they've gotten further then what Venter said at the time.
Why was the Spanish Flu so deadly?
Why are some people immune to HIV? Why do those people tend to be of European descent?
Why is this strain of Pseudomonas fluorescens more able to prevent a plant disease than that strain?
Very recently, why does that dog have curly hair and another dog have short hair and a 'mustache'? Three genes, that on the DNA level are different.
Most of the work just doesn't get publicized except in obscure journals, where only a hundred or so people read the work.
I dunno, I think a farmer who is able to keep their Canola crop growing because of hand-picked bacteria to kill off some fungus/bacteria/nematode/what-have-you is a pretty major thing.
Turn off the bot and the game goes through as before, so I don't think the games have to be dumbed down to make this technology possible.
I hear you on the frustration of making a bot go through a game accurately, I used to do automation for some Xbox360 games.
I think this is a good idea. I have about 30 games that I don't want to put the time into finishing, but I'd love to see how the game progresses.
It might actually make me want to pick up the controller and take over, which is something I wasn't going to do before.