Cutest genome yet

pandaIn the ongoing series of Another Day, Another Genome….we add the giant panda!  By far the cutest genome yet.  Well, ok, I actually haven’t seen the genome yet as the site was down last night when I tried.  But I’m sure it’s adorable. Her name is Jingjing, and she is a 3 year old panda and was also the 2008 Olympic mascot, according to the supplement info.  She’s a supermodel of pandas, I guess.

Hat tip to James and the Giant Panda Corn

The paper is here:  The sequence and de novo assembly of the giant panda genome

The database and sequence is here: http://panda.genomics.org.cn The browser looks nice, but I’ve found some odd implementations.  The ? tools yields the messsage “this tool is empty”. Got the same message from the Config button.  Documentation a bit sparse. Sigh.  More later as I look harder at it.

Update: The browser implementation threw me at first, reminded me of JBrowse but not exactly. As they describe:

We illustrated the panda genome data in a MapView, which is powered by Google Web Toolkit . A new module was developed to browse large-scale short reads alignment. This module enabled users track detailed divergences between consensus and sequencing reads.

Nice.

5 thoughts on “Cutest genome yet

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  3. Max

    I don’t understand why everyone is re-implementing a genome browser, just takes tons of programming resources. Why don’t they stick with Ensembl, UCSC or GBrowse?

    Can’t find anything in this Panda browser… what did you search for? Mapviewer doesn’t work, search for standard gene symbols gives 0 results (HoxA2, HoxA, TP53, etc).

  4. Mary Post author

    Hi Max–

    Yeah, I know what you mean. But there are some issues with the existing technology. You should read the JBrowse paper attached to my post about that, they cover a lot of those. I think probably the most important one is that more of the processing will be shifting to the user’s computer rather than the provider’s server.

    I just loaded up the default Mapviewer page before and zoomed up and down from there, but nothing appears to be loading for me now. I tried to go in by the back door by running a BLAST search and that failed too. I think there must be some issues at the site.

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