What's your problem? Open Thread

q_mark2.jpgWelcome 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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3 thoughts on “What's your problem? Open Thread

  1. azalea

    Hi all,

    I’m wondering is there a gene feature(e.g. exons,introns,UTRs) annotation tool which predicts exons etc. from a genomic sequence?

    It is even better if this tool could use a reference genomic sequence from a homologue of a closely related species with annotated exons and introns.

    I got the to-be-annotated genomic sequence by BLAST using an annotated gene, that’s why I hope what’s already known about the gene could help in annotating the new genomic sequence.

    I’m new to this field, so if I did not make myself clear please leave a comment. Thank you!

    Best,

    azalea

  2. Mary

    Hi azalea–

    I don’t know what kind of genome you need done, but I’m going to point you to a few things that might be useful:

    JCVI Annotation service: http://www.jcvi.org/cms/research/projects/annotation-service/
    On this page you can also examine their annotation training and see the software they use. You might get some leads there.

    There may be some tools around the GMOD (Generic Model Organism Database) project that would suit your needs. Check out this main site, and then browse around the other software (such as Apollo)
    http://gmod.org/

    Other common prediction tools that are used for human/other genomes include:
    AceView: http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/

    N-Scan: http://mblab.wustl.edu/nscan/submit/

    geneid: http://genome.crg.es/software/geneid/index.html

    Genscan: http://genes.mit.edu/GENSCAN.html

    Augustus: http://augustus.gobics.de/

    That should get you started. Let us know if you have success with them. It is nice to know which ones are working for which tasks.

  3. azalea

    Thanks Mary!
    I just read that SGP-2,SLAM and TWINSCAN are programs to predict gene structures using two genomes.
    However, I think one-genome gene predictors like Genscan or geneid could be competent for predicting gene structures in a compact genome like what I am working on (Arabidopsis).
    I’ll have a closer look at these tools and let you know the results.
    Thank you again!

    azalea

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