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

  1. Jeremy

    This is a bit of a cheek I know, but I’m looking for help to answer a question in a recent blog post. The post is at http://jeremycherfas.net/wp/Archive/2008/05/25/framing-a-defect/ and it concerns mutations of a cytochrome P450 gene in some varieties of corn (maize).

    The question is “whether Teosinte and farmer varieties of maize carry the protective cytochrome p450 or the “defective” version”.

    the original papers describing the research are here http://wssa.allenpress.com/perlserv/?request=get-abstract&doi=10.1614%2FWS-07-145.1 and here http://wssa.allenpress.com/perlserv/?request=get-abstract&doi=10.1614%2FWS-07-149.1 but I have no clue how to use the information to search the maize genome databases to find out which is the prevalent “wild type” allele.

    Thanks to anyone who can help.

  2. Mary

    Hi Jeremy–

    Today is a major holiday in the US so we’re all off. But we’ll look into the variations later this week. It is a good question.

  3. Mary

    Hey Jeremy–

    We went looking into this some more, and have some ideas for how you could proceed. I have to say that we agree with you and your blog post–the natural state of this gene is not necessarily a defect :)

    As with most things in bioinformatics, there are a number of ways to tackle this. Here we will point you to a few–but you’ll have to carry the ball from there and keep looking. I’m afraid the bottom line is that we don’t have the full answer. Partly because the data just doesn’t seem to be in the databases, partly because we don’t want to take your project away from you…ahem…

    Ok, so the deal was this: as we looked at those papers, it appeared that the key was the 392 basepair insertion in that resistance gene (Nordby et al). So we thought–well, let’s go get the sequence for that, and the regular p450. But…it didn’t appear to be published in the scientific literature–the reference for that insertion is a poster presentation at a plant conference in 2006 (http://www.maizegdb.org/maize_meeting/2006/). I tried to find evidence of a scientific publication by those authors and didn’t find anything (http://agricola.nal.usda.gov/ and other sources). We tried all our usual sources for sequences GenBank, MapViewer, PlantGDB: http://www.plantgdb.org/ , Gramene: http://gramene.org/, TIGR Maize browser: http://www.tigr.org/tigr-scripts/gbrowse/gbrowse/zma1/ MaizeGDB: http://www.maizegdb.org/ and the MaizeDB: http://www.maizesequence.org/. It wasn’t easy to get to the region of interest. I found Ben1 and Nsf1 in MaizeGDB locus records, at least–not most of the others. I eventually went back to the paper to look for some adjacent markers–which appear to be umc1766 and umc2036. The region between these two markers is where to find that insertion. I ended up preferring the Gramene view of this region (hope this link works):
    http://gramene.org/Zea_mays/cytoview?l=5:1-6365100;h=umc1766. Yeah, it is a big region to hunt for 392 bp.

    What we would do next is obtain this sequence, and locate the p450 genes in it. Some p450s can be found here: http://drnelson.utmem.edu/CytochromeP450.html I would locate likely p450s in that segment, and then start searching the databases with that as my hook. And by searching the databases–I would go to every one that stores plant genomes and ESTs and see if any of them contain the sequence and possibly bigger-than-expected pieces. I would align them against each other (using probably VISTA http://www.openhelix.com/downloads/vista/vista_tutorialhome.shtml, or maybe Clustal–depends on how big and how many you have). I would try to find evidence of that 392 bases in there.

    We are considering the possibility that this is the result of a transposition event–and an incomplete excision of a transposable element. We would look at TE information to see if the sequence looks like any of the known ones. A nice spot might include: http://maize.tigr.org/repeat_db.shtml But that might take a little bit more sleuthing as well.

    Here’s the really short answer: find those authors on the insertion poster reference and ask them. But I’ll betcha it is proprietary: http://www.patentdebate.com/PATAPP/20070214515 (that’s them). Actually–looks like there’s a sequence alignment in that patent….That sequence may be disclosed in there. And it may be possible to get a look at it….Ask your favorite science librarian how to do that. And then go looking for that bit in the sequence databases–including all ESTs and even the trace archives off the sequencing projects. Check the strains on the sequence submission to find out what variants they are.

    Update: I just realized the USPTO record had more info, include the accession numbers for the p450s: from that patent link, click the link at the top for “View on USPTO site” and check that out. Those would be good hooks into the EST and sequence databases.

    Good question, that was fun, actually. Plants are tougher than humans to find what I am looking for, I have to say….

    EDIT: I went to look at this again for a discussion I was involved in elsewhere, and found the patent site was gone. The other way to find this record is right at USPTO:
    http://appft1.uspto.gov/netahtml/PTO/srchnum.html and search with 20070214515

  4. Jeremy

    Wow! Thanks so much for making that huge effort. I’m way out of my depth here, but I know a man who might not be. I’ll try and interest him, just for fun. and I’ll try the direct approach too. I’ll probably follow up on my blog, and I’ll try and remember to alert you.

  5. Mary

    It was a fun way to spend an afternoon. We really enjoy this kind of sleuthing. And we like to do these to keep our skills sharp–it really was a good exercise.

    Do keep us posted.

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