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Biology Help Desk: Volume 4

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  • Your statement that short ion torrents read lengths are 10x longer than they need to be makes no sense whatsoever. That's true if you are ok with a 4% error rate in the genome .. and missing crucial mutations.

    • I admit that didn't check at the time for the exact length of an IonTorrent read, but the figure given was 200-400x. With the fifth-generation SOLiD system, a read length of just 22 bp is sufficient for human variability and disease identification studies—and coverage solves pretty much all error-related problems. The lab I work in made the decision to go with a SOLiD 5500XL system after about two years of shopping and negotiating with half a dozen different vendors, and the deciding factor was the im
  • Hi and thanks for the offer to answer questions. I'm going to repost something I wrote in the google science fair thread:

    Ok slashdotters, I've had no luck getting this question answered elsewhere so I might as well try here. My son is very interested in coding. He's competent in Java and he's picking up c quite well. He's taken an interest in GPU programming and I know over the next year he will do OK with those concepts too (I've been able to get both OpenCL and CUDA code up and running). In other words,

    • The study you're describing sounds like a fairly challenging task for a student because of the "determined where on a protein they would attach" part. That step alone requires an advanced understanding of chemical kinetics and two or three years of university-level calculus, as well as access to a serious high-performance computing cluster. Because of the calculus requirement, it's generally considered outside of the realm of bioinformatics—it's also something that pharmaceutical companies do religiou
      • by superid (46543)

        Thanks for the info. I will try to find some medical journals. We have a family member with Parkinson's so we might start with that. As far as the statistics, yes, he is taking a class and luckily his mom is a statistician :)

  • is everyone clinging to python2 forever?

    • I'm not a pythonista, although many bioinformaticians are. As I understand it, the spread of mentalities amongst CS-trained bioinformaticians is the same as amongst any software engineers—some say 'upgrade at once', others are more pragmatic and will write new things in Python 3 but don't bother upgrading old projects as long as Python 2 is supported, and there's a tiny handful of programmers who are happy right where they are in Python 2 and turn off automatic updates whenever they get a chance.

      Bi
  • There's now a story out that says human genome sequencing could be done rapidly and for about $1,000. I have been trying to get a medical test that's just sequencing a single gene (CPT2). The test takes 4-6 weeks to get results and costs $1100. Do you have any insight why this might be? Is there more work for the single-gene sequencing that doesn't get factored into the full genome price?

    • That sounds like a combination of cost of labour and older chemistry. The IonTorrent system described was just put on the market and costs $149,000 for the hardware, so it'll be a while before most places have them. Further, for that system, the $1000 price tag is just the cost of the chemical reagents as sold by the manufacturer; the human labour cost is actually pretty substantial. The time requirement does sound a little high, but that probably factors in a processing queue and transit time.
      • I'm not a bio guy, but I'm curious to know what one can learn about themselves using an OpenPCR. [openpcr.org]

        Could a layperson, for example, use one to determine their risk of disease with strong genetic factors? A criticism in the Wired article stated that, "The thermal-cycling machine is only a small piece of what's important about PCR and what's required to do it. You need so many other things, including access to chemistry (a reference to proprietary reagents) that's way harder to hack than the machinery itself.
        • A thermal cycler does nothing more than heat and cool a little metal block to a series of set temperatures in a short loop, hundreds of times. To perform PCR, you need nucleotide triphosphates (the actual nucleotides that the new strand will be built with), DNA polymerase (the enzyme that performs the actual DNA replication), several different salts in a very precise mixture, perfectly clean water, a micropipette (it sounds like it's from 50s sci-fi but isn't), the extracted DNA (kits for this cost a hundre
    • Update on this: the IonTorrent system isn't quite released yet, it's coming out later this year. Prior to it, a typical full-exome sequencing job (all the functional parts of genes, like all the code without any headers) costs about $12000, in academia.
  • Hi,

    I followed with interest the news of the bacteria that can use arsenic. Later (if I understood correctly) it turned out to be less impressive than initially thought, and can only substitute arsenic for a small percentage of the phosphorus it needs.

    I was wondering if there have been any attempts to create such bacteria by artificial selection. Is there any sort of targeted effort along those lines to try to determine in what conditions can life exist?

    Thanks!

    • I don't know of any such strains personally, but experiments to produce extremophiles certainly exist. (Here's one example [asm.org]: high-pressure E. coli.) A search query like this one [google.com] is probably a good place to start.

      This all being said, for us to find life on other planets that exists in some of these forms, there has to be a plausible path backing up the process; I think a lot of people don't quite get this. Just because you can breed, say, extremely radiation-resistant bacteria in a lab doesn't mean that life

      • I don't know of any such strains personally, but experiments to produce extremophiles certainly exist. (Here's one example: high-pressure E. coli.) A search query like this one is probably a good place to start.

        Cool, thanks

        This all being said, for us to find life on other planets that exists in some of these forms, there has to be a plausible path backing up the process; I think a lot of people don't quite get this. Just because you can breed, say, extremely radiation-resistant bacteria in a lab doesn't mea

        • From a xenobiology standpoint, it's not really that useful to know that arsenic-tolerant bacteria can evolve on Earth, no. It's only a big deal because organisms here have a really bad habit of mistaking it for phosphorus and dying as a result. They have different (but similar) chemical properties, and this can mess up metabolic pathways (series of biochemical reactions) that were finely-tuned for the nature of phosphorus. Phosphorus is a wonderful element, capable of many things, but it's hardly as if life

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