“What’s Your Problem?” Open Thread

Sorry for the delay–internet problems all day! We will still answer your questions this week–let’s roll it into Friday to make up for the down time.

Welcome 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. 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, chime in.

The “WYP” thread will be posted every Thursday and remain at the top of the blog for 24 hours.

You can keep up with this thread by remembering to check back, by subscribing to the RSS comments feed to this WYP post or by subscribing to be notified by email of new comments to the post (use checkbox at end of comment form, you can unsubscribe later). If you want to be notified of future WYP posts (every Thursday), you can subscribe to the WYP feed.

8 thoughts on ““What’s Your Problem?” Open Thread

  1. João Fadista

    Hi,

    I would like to know of some tools where I can paste a fasta sequence file and then the output would be like the number and type of repeats there, the %GC content and other possible features as well.
    P.S. A tool that I can use for free :)

    Best regards,
    João Fadista

  2. João Fadista

    Thanks for the useful information.
    I know that “What´s your problem?” day is over but I would also like to know if know of a generic karyoview tool like Ensembl has but where I can choose the size and the number of chromosomes to plot along with my own features.

    Best regards and thanks in advance!

  3. Mary

    Hello João–

    I don’t know if this will do everything you want (it isn’t as good for adding your own data as other tools), but the NCBI Map Viewer will let you show a region and add different maps.

    For example, in human there is an ideogram map. If it isn’t in your default view you can go into “Maps and Options” and add it, move it over, and then show the other maps you are interested in.

    On the left side of the page you can chose the region to display (with the “regions shown” boxes).

    I’m going to paste a URL here (not sure if it will work for you) where I set up a region with some genes on a second map.

    http://www.ncbi.nlm.nih.gov/projects/mapview/maps.cgi?TAXID=9606&CHR=17&MAPS=ideogr%2Cgenes-r&QSTR=tp53+AND+gene%5Bobj_type%5D&QUERY=uid%2811096912%29&BEG=900K&END=13%2C900K&thmb=on

    I’m going to look at some GBrowse tools to see if they have them, too–I think they might. Are you interested in human mostly?

  4. Mary

    Yes, the GBrowse tool can do this as well. If you read my post on the SNPedia stuff in GBrowse it shows a good example of how to do this.

    SNPedia created a place for people to pull their own data, and view it on the HapMap display. And as long as you have ideogram checked in the “Tracks Display”, you can have that with your own stuff. Use the tracks display to choose what you want to show. You can also learn how to build these custom tracks to show.

    Read this post, I think it will illustrate that:
    http://www.openhelix.com/blog/?p=82

    And this is for human, but there are other instances of GBrowse for other species, I know.

  5. João Fadista

    Thanks once again but my problem persists.
    I am working with a pre ensembl species which is not yet available on other public GBrowsers. So a general ideogram/karyoview tool that isn´t species constrained would be good to have.

    Best regards,
    João Fadista

  6. Mary

    Ah, I see. But GBrowse is a generic tool that you can use to build that. Go here: http://www.gmod.org/GBrowse

    It is part of the GMOD project, which is Generic Model Organism Database.

    They give you all the tools to build this for your own species of interest.

Comments are closed.