"What's Your Problem" Open Thread

WYPWelcome to the “What’s Your Problem?” (WYP) open thread. The purpose of this entry is to allow the community to ask questions on the use of genomics resources. Think of us as a virtual help desk. If you have a question about how to access a certain kind of data, or how to use a database, or what kind of resources there are for your particular research problem, just ask in the comments. OpenHelix staff will keep watch on the comment threads and answer those questions to the best of our knowledge. Additionally, we encourage readers to answer questions in the comments too. If you know the answer to another reader’s question, please chime in! The “WYP” thread will be posted every Thursday and remain at the top of the blog for 24 hours.Questions or problems asked on Thursday will be answered on Thursday to the best of our ability. You can leave questions on other days of the week, but the answer might not come that day.

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6 thoughts on “"What's Your Problem" Open Thread

  1. gsgs

    I’ve read that sequencing is becoming much cheaper, so can we expect lots of new sequences in the near future ? (~2009)

  2. Mary

    Yes, we can expect TONS of new sequence soon. The new “next-gen” or “next generation” sequencing technologies are in the hands of people who are working hard with them now. They are still working out some bugs, and they are still trying to figure out which ones work best for which purposes, but they are definitely on the way.

    Here’s a brief article about some of the issues:
    http://www.in-sequence.com/issues/1_44/features/143486-1.html

    They are running into problems with how to handle the data. And there are concerns about moving the data around on these unprecedented scales. It may require new strategies for tools that are built.

  3. Theodore Horoschak

    Where do I go to find out which new sequencing technologies are out there already?

    Also, I read the brief mutation web page and utah.edu. I find the DNA ploymerase “mistake” curious? All of these little suckers are deterministic machines, but at the molecular level. How can it make a “mistake”? What goes wrong. Do they know?

  4. Jennifer

    Hi Theodore,

    ?1. There is lots of information on next-generation sequencing available online & there is an upcoming conference if you are really into learning.

    Online, I’d suggest that you could also go to the websites of the major companies (Applied Biosystems, GE Healthcare, Helicos BioSciences, Illumina/Solexa, Reveo, Roche/454 Life Sciences and VisiGen Biotechnologies) & read about each of their technologies in their own words. You could also go to http://www.technologyreview.com/ registering & then search on “next-generation sequencing” – they have lots of articles. Also at http://www.healthtech.com/sqe/overview.aspx, they give some info & announce the “Exploring Next-Generation Sequencing” Tech Expo occuring in Sept.

    ?2. I think you are referring to http://learn.genetics.utah.edu/units/disorders/sloozeworm/mutationbg.cfm, which is a cool basic description. As you say, DNA polymerase is a machine & just like any manufacturing machine, little physical disturbances during production can create errors in the product. Sometimes the machine grabs the wrong thing & inserts an incorrect base, sometimes it slips a bit on its template. Check out this site for a bit more detailed description http://tinyurl.com/polymistakes.

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