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
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. A tab-delimited version of this file and other related files
are available within the same directory.
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 (and
possibly at the budding ChlamyBase.org website).
Those of you who have been waiting awhile for these, thanks for your
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
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