What's Your Problem? OpenThread

wyp_q_mark2_thumbnailWelcome 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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4 thoughts on “What's Your Problem? OpenThread

  1. StephS

    I am having some challenges with gap closure of a genome with a large number of repetitive elements, following contig assembly. I have about 10 gaps which are flanked by these repetitive elements found throughout the genome. Can you recommend strategies? I tried Projector 2 and was not successful in generating more than a few unidirectional primers. All the other primers generated had homology to numerous other loci dispersed throughout the genome.

  2. Jennifer

    Hi StephS,

    Genome assembly is far from my field of expertise, but I did attend a session on it at the recent International Biocuration Conference. Groups that are creating publicly available assembly software include:

    GMOD http://gmod.org/wiki/Main_Page
    J. Craig Venter Institute (formerly TIGR) http://www.jcvi.org/
    Joint Genome Institute http://www.jgi.doe.gov/
    Sanger http://www.sanger.ac.uk/
    University of Washington’s Department of Genome Sciences http://www.gs.washington.edu/

    I have heard of several genome annotation projects that received essential help from the excellent people involved with GMOD, and I am under the impression that the other groups also are willing and able to help researchers. I’d suggest emailing them for expert advice.

    If you’d like to check out some of the software that I heard about at the conference (and elsewhere), here’s a short list:
    Appollo http://apollo.berkeleybop.org/current/ (from GMOD)
    Artemis and ACT http://www.sanger.ac.uk/Software/Artemis/ http://www.sanger.ac.uk/Software/ACT/ (from Sanger)
    HAVANA http://www.sanger.ac.uk/HGP/havana/ (from Sanger)
    MANATEE http://manatee.sourceforge.net/ (from JGI)
    MicroScope http://www.genoscope.cns.fr/agc/mage/wwwpkgdb/MageHome/index.php?webpage=microscope (from Genoscope)
    PATHEMA http://pathema.jcvi.org/Pathema/ (from JCVI)
    RepeatMasker http://www.repeatmasker.org/ (from Institute for Systems Biology and used by NCBI & UCSC Genome Browser)
    Sybil http://sybil.sourceforge.net/ (from JCVI)

    I also found this discussion forum that might have useful info (I searched on ‘contig’):
    Protocol Online – a database of research protocols http://www.protocol-online.org/

    Please let us know what eventually works for you. Other readers – if you have a suggestion for StephS, please feel free to chime in!

  3. Mary

    Hi StephS–

    I’m about to get on a plane and I’ll think more about this, but one thing that might help in this case is the UCSC In Silico PCR tool. If your genome is in UCSC you can use that to check your primers around the genome.

    If your genome isn’t in there you might have to download and run a local copy. But that might work for you?

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