These exercises use the Apollo Gene Annotation system available
at
http://apollo.berkeleybop.org/current/index.html.
Install Apollo and data, load and save demo data.
-
On the Mac's, you can run Apollo from the folder /nfs/ecg/Applications/Apollo. You can find this folder by clicking on the mac_hd icon on the upper left in the Finder window.
On the PC's, you will need to download Apollo from the WWW site above, and run it from your Desktop or Downloads folder.
- Once you have installed Apollo, you should copy
the apollo data to your directory. On the Mac's, the data is
in /nfs/ecg/data/apollo. Drag the /nfs/ecg/data/apollo
folder to your desktop or home directory.
On the PC's, you will need to map a network drive from
courses.cshl.edu:/ecg. You can mount the drive with guest access.
There are two distinct problems on the WWW site. If you are doing
problem 'A', which involves annotating the TBX18 gene, you
will need to work with the h_tbx18.fa
and h_tbx18.gff files. If you are working on problem 'B',
you will use orang.fa and orang.gff.
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Once you have installed Apollo and the data, start
up Apollo. When Apollo asks for a dataset to start, DO
NOT use the default provided. Tell Apollo that you
want ENSEMBL GFF Format, and you will be given two lines to
fill in, the Ensembl GFF format file, and the Sequence
file. Use the Browse option to find your local copy of
the apollo/h_tbx18.gff or apollo/orang.gff
and apollo/h_tbx18.fa or apollo/orang.fa files.
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Then, save your annotations (File Menu). Save them as Game
XML with a filename h_tbx18_work.xml / orange_work.xml.
Be sure to save the data on your local home directory or Desktop,
e.g. /Users/your-id/orang.xml on Macs.
-
Quit Apollo.
Now follow the instructions for building the gene models in the handouts.
The proteins you find can be compared to the TBX18 or Orang Zn finger sequences.
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