[Chlamydomonas] v3 annotations mapped to v4 genome assembly and Augustus models (again)

[Erik F. Y. Hom]

Dear Chlamy Community,

I was told that the links in my previous email did not show up!  My  
apologies; I've spelled them out below in case your email viewer can't  
handle the hyper-linked text.  In general, you can go to http://erik.freshboom.com/chlamy/ 
  and navigate from there (it's a minimalist's website at the moment).

Sincerely,
erik


---
Dear Chlamy Community,

This is to announce that JGIv3 Chlamy genome annotations have been  
mapped to the current AUGUSTUS gene models for the v4 Chlamy genome  
assembly (a.k.a. the AUGUSTUS "update 5/UTR5" gene models).

For those who attended the Chlamy '08 meeting, you may recall mention  
of (an earlier set of) these gene models, which were generated in  
collaboration with Mario Stanke (the author of AUGUSTUS) and Chun  
Liang: http://augustus.gobics.de/predictions/chlamydomonas/

Although the recently release JGIv4.0 gene models incorporated the  
AUGUSTUS gene predictions as a source of input, the resulting models  
can differ significantly in the details and the two sets should be  
viewed as distinct if not complementary.  The advantages of the  
AUGUSTUS model set include simultaneously-consistent alternative  
transcript and UTR predictions; a possible disadvantage (anecdotally)  
is that some of the current AUGUSTUS models may fuse two or more  
genes.  Regardless, improving the AUGUSTUS Chlamy gene models remains  
an active and ongoing project.

If you'd like to use the AUGUSTUS models, you now have some functional  
annotations to work with, courtesy of the community's efforts on v3 of  
the Chlamy genome.  You may download an Excel file for these mappings  
here (http://erik.freshboom.com/chlamy/CRv4_AnnotationMappings/JGIv3_to_CRv4AugustusU5.map20090407.xls 
)  A tab-delimited version of this file and other related files are  
available within the same directory (http://erik.freshboom.com/chlamy/CRv4_AnnotationMappings/ 
).

For more details about these results, please refer to the README page.

These mapping results along with additional functional annotation data  
will be available from the AUGUSTUS Chlamy website within the next few  
days.  Regular updates to these annotations will be posted over the  
next couple of weeks: for download at the freshboom.com site and for  
more user-friendly interactive use at the AUGUSTUS website.   
Importantly, Elizabeth Harris and I are working hard to make sure all  
the available genetic linkage markers/data/references are incorporated  
with these mapped annotations;  when we're done, we will post them  
(along with any editorial corrections/additions).

These mapped annotations will also be available soon in association  
with the AUGUSTUS models at the JGI Chlamy v4 genome browser (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html 
) (and possibly at the budding ChlamyBase.org website (http://www.chlamybase.org/) 
).

Those of you who have been waiting awhile for these, thanks for your  
patience!

If you have any questions or comments, feel free to contact me.  In  
particular, if you notice any errors or have any corrections/additions  
to Your Favorite Gene(s), please kindly let me know; I will make sure  
it gets fixed and reflected in future updates, for the benefit of the  
Chlamy community.

Sincerely,
erik


---
Erik F. Y. Hom
Postdoctoral Fellow, Murray Lab
MCB, Harvard University
52 Oxford St., NWLabs 458.40-8D
Cambridge, MA 02138, USA

Lab: +1-617-496-1384 | -1489
Fax: +1-617-496-1541