Comments on: Transposons, Browsers, and Annotation, oh my! http://www.biofortified.org/2009/03/transposons-browsers-and-annotation-oh-my/ Stronger plants, stronger science, and stronger communication. Wed, 08 Feb 2012 17:17:15 +0000 hourly 1 http://wordpress.org/?v=3.0.1 By: Leonardo Galindo http://www.biofortified.org/2009/03/transposons-browsers-and-annotation-oh-my/#comment-17286 Leonardo Galindo Wed, 10 Nov 2010 22:03:45 +0000 http://www.biofortified.org/?p=231#comment-17286 Hi, I am a research tech working at the University of Alberta and I am characterizing the flax proteome transposons. I have done a series of blast searches on the full protein set (about 47000) genes and have found trademarks of transposons in over 2000 sequences. However some of them are a bit confusing. I have many hits to RNA helicases, and the only link that I can make is with Helitrons, but Helitron helicases are really DNA and not RNA helicases...or at least that is what I think, so I do not know if a hit to one of these helicases is really related to a transposon or just a hit to an helicase related to another process... any ideas? thanks Hi,
I am a research tech working at the University of Alberta and I am characterizing the flax proteome transposons. I have done a series of blast searches on the full protein set (about 47000) genes and have found trademarks of transposons in over 2000 sequences. However some of them are a bit confusing. I have many hits to RNA helicases, and the only link that I can make is with Helitrons, but Helitron helicases are really DNA and not RNA helicases…or at least that is what I think, so I do not know if a hit to one of these helicases is really related to a transposon or just a hit to an helicase related to another process… any ideas?

thanks

]]> By: Frank N. Foode at Maize Genetics http://www.biofortified.org/2009/03/transposons-browsers-and-annotation-oh-my/#comment-297 Frank N. Foode at Maize Genetics Thu, 19 Mar 2009 08:29:01 +0000 http://www.biofortified.org/?p=231#comment-297 [...] flight was delayed, so I missed the first part of the conference. Luckily someone filled me in on what happened. Apparently I’m 1.4 percent Helitron! Good [...] [...] flight was delayed, so I missed the first part of the conference. Luckily someone filled me in on what happened. Apparently I’m 1.4 percent Helitron! Good [...]

]]> By: Maize genetics http://www.biofortified.org/2009/03/transposons-browsers-and-annotation-oh-my/#comment-286 Maize genetics Tue, 17 Mar 2009 04:47:54 +0000 http://www.biofortified.org/?p=231#comment-286 [...] add to Karl’s excellent coverage of the Maize Genetics Meeting, I’m writing some summaries of selected talks over at Genetic [...] [...] add to Karl’s excellent coverage of the Maize Genetics Meeting, I’m writing some summaries of selected talks over at Genetic [...]

]]> By: Anastasia Bodnar http://www.biofortified.org/2009/03/transposons-browsers-and-annotation-oh-my/#comment-285 Anastasia Bodnar Tue, 17 Mar 2009 03:47:32 +0000 http://www.biofortified.org/?p=231#comment-285 I've found the Arabidopsis site http://www.arabidopsis.org/servlets/Search?action=new_search&type=germplasm where you can find (and order) mutants for a particular trait. There's gotta be something similar for maize! I’ve found the Arabidopsis site http://www.arabidopsis.org/servlets/Search?action=new_search&type=germplasm where you can find (and order) mutants for a particular trait. There’s gotta be something similar for maize!

]]> By: Karl Haro von Mogel http://www.biofortified.org/2009/03/transposons-browsers-and-annotation-oh-my/#comment-283 Karl Haro von Mogel Tue, 17 Mar 2009 02:12:10 +0000 http://www.biofortified.org/?p=231#comment-283 There's a lot of stuff on David's site that needs cataloging - which we can do bit by bit, he's got no problem with it. I'm not sure about places that have records of maize TDNA libraries. As for arabidopsis, you could try here: http://signal.salk.edu/tabout.html I think they plan to complete it by 2010, that's one year away... maybe there's something useful there? There’s a lot of stuff on David’s site that needs cataloging – which we can do bit by bit, he’s got no problem with it.

I’m not sure about places that have records of maize TDNA libraries. As for arabidopsis, you could try here: http://signal.salk.edu/tabout.html I think they plan to complete it by 2010, that’s one year away… maybe there’s something useful there?

]]> By: Anastasia Bodnar http://www.biofortified.org/2009/03/transposons-browsers-and-annotation-oh-my/#comment-282 Anastasia Bodnar Tue, 17 Mar 2009 01:36:21 +0000 http://www.biofortified.org/?p=231#comment-282 What a great summary - I think you capture some of the craziness and wonder that comes from having that many maize geneticists all in one place. A few random thoughts: Heliotrons are just so cool, jumping around, moving bits of genes to new places in the genome. I really like David's "natural GMO" series. I wonder if we could get a linked summary of them to make it easy for people to find the articles? I wish MaizeGDB would switch to a Wiki or some other format. I find it very difficult to search for things on their site, although you can tell they are trying. Most importantly, we need to get more info in one place. For example, I know there exist many sets of mutant maize lines that are known to have, say tDNA insertions in iron transport and storage related genes (which is what I want) but I don't have any idea where to start looking. It should be at MaizeGDB! You wouldn't happen to know where I can find them, or similar lines for Arabidopsis, would you? What a great summary – I think you capture some of the craziness and wonder that comes from having that many maize geneticists all in one place. A few random thoughts:

Heliotrons are just so cool, jumping around, moving bits of genes to new places in the genome. I really like David’s “natural GMO” series. I wonder if we could get a linked summary of them to make it easy for people to find the articles?

I wish MaizeGDB would switch to a Wiki or some other format. I find it very difficult to search for things on their site, although you can tell they are trying. Most importantly, we need to get more info in one place.

For example, I know there exist many sets of mutant maize lines that are known to have, say tDNA insertions in iron transport and storage related genes (which is what I want) but I don’t have any idea where to start looking. It should be at MaizeGDB! You wouldn’t happen to know where I can find them, or similar lines for Arabidopsis, would you?

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