2. Collect proteins that do not induce an immune response. These
proteins will represent the “negatives” (see Note 12).
3. Create a file (e.g., positives.fasta) containing the positive
sequences in a FASTA format.
4. Create a file (e.g., negatives.fasta) containing the negative
sequences in a FASTA format.
5. Copy the entire template_species directory to a user-named
directory (e.g., training).
6. Copy FASTA files from steps 3 and 4 into install_dir/vacceed/training/proteome.
7. Copy “toxoplasma.ini” to “train.ini”.
8. Add a new line to startup.ini located in install_dir/vacceed/
start/:
train< Neospora caninum vacceed/start/config_dir
9. Edit train.ini to match the following:
work_dir="install_dir/vacceed"
species_dir="training"
email_url="your_email@address" (user e-mail address)
proteome_fasta="positives.fasta" (as per step 3)
prot_id_prefix="xx" (needs to match the sequence identifier)
10. Modify [Resources] in train.ini if required; for example,
remove any resource not installed or required.
11. Change directory to install_dir/vacceed/start in a commandline terminal.
12. Enter the command: perl startup train (where “train” is as per
step 8).
13. Copy the file “evidence_profiles” from install_dir/vacceed/
training/pipeline/evidence/output to install_dir/vacceed/
training/pipeline/evidence/training_files.
14. Rename evidence_profiles to a user-defined name (e.g.,
neospora_profiles).
15. Add “,YES” to the end of each row in the new training file
(exclude the first row). The “YES” is the required target label
for the positives.
16. Edit train.ini to match the following:
proteome_fasta="negatives.fasta" (as per step 4)
17. Change directory to install_dir/vacceed/start in a commandline terminal.
18. Enter the command: perl startup train.
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