[DEW-users] Just_Annotate_My public beta release

[<Ale...@cs...>]

Dear all,

I'm emailing you because you expressed an interest to one of the Just_Annotate pipelines, and now that John/Yannick outed me on Twitter it was a good kick to get a release candidate out.

There are a total of three software which where inspired by the NESCent community curation working group and we've been using for:

  *   structural (feature) annotation: where is the gene? -> Just_Annotate_My_Genome<http://jamg.sourceforge.net/> (JAMg)
  *   functional annotation: what could this gene do? -> Just_Annotate_My_Proteins<http://jamps.sourceforge.net/> (JAMp)
  *   expression studies from large amount of RNA-Seq (e.g. 41 libraries/HiSeq lanes) -> DEW<http://dew.sourceforge.net/>

The amount of testing (and documentation) that has been done for being used by other people is JAMg > JAMp > DEW.
The complexity of the software is JAMp < DEW <  JAMg

Generally you will need to have (someone with) good IT skills to run programs that require MPI. The JAMp software is based on running HHBlits on a high-performance cluster. I tried to write a small script that will work on local machines (prepare_annotations_hhblits.pl) but ran out of time for testing it (should work...).

If you are feeling brave, you can the release candidates from here:
https://sourceforge.net/projects/jamg/files/RC
https://sourceforge.net/projects/jamps/files/RC<https://sourceforge.net/projects/jamps/files/RC/>
https://sourceforge.net/projects/dew/files/RC

Email lists to subscribe for support (to receive and give):
https://lists.sourceforge.net/lists/listinfo/jamg-users
https://lists.sourceforge.net/lists/listinfo/jamps-users
https://lists.sourceforge.net/lists/listinfo/dew-users

I'll be away next week but I hope that after that I will focus on fixing any errors you reports and better documentation. Your beta-testing efforts are much appreciated.

Augustus 3
JAMg relies heavily on Augustus and a lot of work has been investing in circumventing various bugs and implementing some new methods for hint scoring. Please note that the current version of Augustus used is 2.7 (May 2013), I hadn't had the time to test the new version 3 (February 2014). One of the major improvements Mario has done is the prediction on simultaneous genomes (that have been pre-aligned). As I haven't tested, I didn't want to delay the JAMg version. One major issue with Augustus 3 and JAMg however is that JAMg is released under the Apache license ('mostly do what you want but no one can sue us if you misuse it' )but Augustus 3 under the incompatible (viral) GPL. So until Augustus 3 is licensed under the Artistic license again, we can't support it.

many thanks and have a great Easter :-)
a

--
Dr. Alexie Papanicolaou

Phone: +61(0) 2 6246 4511| Mobile: +61 (0) 46 85 81 247
CSIRO Ecosystem Sciences, GPO Box 1700, Canberra 2601, ACT, Australia

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