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.

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6 thoughts on “What's your problem? Open Thread

  1. Chris

    I’m looking for a similarity plot tool. I want to input a MSA, and have a graph drawn of %identity (with a choice of window size for calculating % identity).
    It’s for use with DNA sequences of about 200kb.

    Something “simple” would be nice!


  2. Trey

    Have you looked at mVISTA?

    From the about page:

    mVISTA has a clean output, allowing for easy identification of sequence similarities and differences, and is easily configurable, enabling the visualization of alignments of various lengths at different levels of resolution. It is implemented as an on-line server that provides access to global pairwise, multiple and glocal (global with rearrangements) alignment tools.

    You’ll need to open the settings window in VISTA to set thresholds. Check out the tutorial too if you need some pointers.

    I’ll check around for some other tools too.

  3. João Fadista


    I have a question related to the possibility of analysis of raw intensity data of array CGH experiments.

    After the analysis of 2-color array CGH data with the usual “standard” protocol (transform raw intensities in log2ratios, normalize, segment the data and call CNVs with some chosen criteria) I want to know the true copy number status of my CNVs, without further experiments. Every array CGH study reports the status of copy number variations in relation to the reference sample but is it possible to know the true copy number status?

    I tried three inconclusive approaches:

    1º – Since my experiment has 24 arrays with the same common reference (in Cy5), I averaged the Cy5 raw intensities of the probes for these 24 arrays and then plotted them across the genomic regions queried. When looking at the plots I tried to see if, for the CNV regions found, there is a significative increase or decrease in the value of the intensities of the probes compared to the neighbouring normal regions.

    2º – Segmented the raw intensities (both test Cy3 and Cy5 reference samples) instead of segmenting the normalized log2ratios. The segments found in both kind of samples were not the same as in the “standard” protocol.

    3º – Made t-tests and Mann-Whitney tests comparing the distribution of the raw intensities (both Cy5 and Cy3) of the CNV regions with the normal copy number regions immediately upstream and downstream of them.

    Is this quest for assessing the true copy number status a lost case?

    Best regards and thanks in advance,
    João Fadista

  4. Mary

    Hello João–

    We are seeing a lot more questions about copy number variations lately, I’m not sure anyone has solved it conclusively. But I will point you to a couple of places that have this type of data and you may compare your methods to theirs.

    UCSC Genome Browser: the human track called “Structural Var” offers a number of different types of variations. Some of that data comes from:

    Database of Genomic Variants which will provide access this data as well. If you search here you will find results that link to the papers which will describe their approach.

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