From: Mason Meyer <mmeyer20@uncc.edu>
Date: Fri 12/5/2014 11:05 AM
To: Gordon Beattie <BeattieGS@cardiff.ac.uk>
CC: "Loraine, Ann" <Ann.Loraine@uncc.edu>
Subject: IGB update on Drosophila version 6 annotations and genome

Hello,

Last month you wrote asking about whether (and when) the IGB team would update the Drosophila genome in IGB to the latest version - version 6, released July 2014.

I just wanted to let you know that we’ve posted the new fruit fly genome in the IGBQuickLoad.org site. I’m sorry for the long wait!

Now, if you start IGB and click the fruit fly image on the start screen, you will go directly to the July 2014 (version 6) release of the D. melanogaster genome. Also, the latest gene models from Flybase will load automatically.

However, you can still access the older genome version using the menus in the Current Sequence tab (on right of IGB window.)

We have not yet thoroughly tested the new genome sequence and annotations in IGB and will be doing that in the coming weeks. In the meantime, if you notice any problems, I’d be grateful if you would let us know.

Once we’ve completed testing, we’d like to make an announcement to the Drosophila research community. If you could recommend a forum where we could reach many people, we'd appreciate the pointer!

Best wishes,

Mason Meyer

From: Gordon Beattie <BeattieGS@cardiff.ac.uk>
Date: Tuesday, November 11, 2014 at 12:22 PM
To: "Loraine, Ann" <Ann.Loraine@uncc.edu>
CC:Mason Meyer <mmeyer20@uncc.edu>, Nolan Freese <nfreese@uncc.edu>
Subject: Re: D. melaogaster Release 6

Hey Ann, thanks for the response!

I've also had difficulties with the FlyBase annotation files, and use the UCSC version when I can.

That would be fantastic! That will enable us to get on with some bits of what we want to do.

Oh no need to apologise, thanks so much for taking the time to try and suss out FlyBase's cryptic gene models! It would be great to have an update on how the process is going.

Best wishes,

Gordon

From: "Loraine, Ann" <Ann.Loraine@uncc.edu>
Date: Tue 11/11/2014 11:40 AM
To: Gordon Beattie <BeattieGS@cardiff.ac.uk>
CC:Mason Meyer <mmeyer20@uncc.edu>, Nolan Freese <nfreese@uncc.edu>
Subject: D. melaogaster Release 6

Hello,

It is nice to hear from you.

Yes, I’ve been hoping to get the new genome and gene models into IGB.

It was easy to get the sequence, but getting the gene models has been harder - mainly because I’ve been having some problems decoding the file format FlyBase uses to distribute the gene models. So I’ve been waiting for UCSC Genome Bioinformatics to import the new gene models into their system. Once they do that, I can very easily get the gene models in “bed” format and show them in IGB. However, as you and a few other people have asked about this, we could look at it again and maybe give decoding FlyBase’s gene models file another try. Alternatively, I might be able to get the data from RefSeq or Ensembl somehow.

I could set up a new Drosophila site with just the sequence data pretty easily - would that be useful?

I’m sorry for the delay! I definitely would like to support the new annotations and genome as they appear to be a big improvement!

Mason, would you make a note of Gordon’s email and make sure that we keep him up-to-date on our progress?

Best wishes,

Ann