What’s Your Problem? Open Thread

wyp_q_mark2_thumbnail1Welcome 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.

We’d also like to invite resource providers to let us know if they have something new to talk about, or something they want to mention to the bioinformatics community. We’ve had some people email us because they weren’t sure if they should post something, and we want to say that’s fine.

So What’s Your Problem? And What’s Your Solution? :)

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2 thoughts on “What’s Your Problem? Open Thread

  1. gsgs

    I’m trying to find the longest common
    nucleotide subsequences in 2 large sets of
    sequences.
    E.g. genbank gbpri (~6GB) and gbvrl (~3GB).
    Someone with much RAM must already have done it

  2. Jennifer Post author

    Hi GSGS,

    I have not done a lot of such comparisons, but my first thought when I read your question is to suggest using VISTA http://genome.lbl.gov/vista/index.shtml, which is a great alignment resource that can handle all sorts of tough analyses. We’ve got a full tutorial http://www.openhelix.com/cgi/tutorialInfo.cgi?id=81 , free for you to watch, on VISTA’s capabilities & how to use it.

    To get further ideas for your problem, I did what I always do – went over to NCBI & search on ‘all databases’ for the sequence IDs you provided. The ‘gbvrl’ search brought up this reference:

    PLAST: parallel local alignment search tool for database comparison
    BMC Bioinformatics. 2009; 10: 329.
    PMCID: PMC2770072 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2770072/?tool=pmcentrez

    I’d suggest you check out the paper & maybe follow up with the authors & see if they have any advise/data for you.

    Best of luck!

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