All files and related dependencies of the LB1 HMM project will be saved here.
Important directories: ~/projects/hmm_LB1/ /media/sf_shared_linux
To rerun the analysis, do the following:
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Obtain the databases as indicated by the method section. Process and parse them with the help of the notebooks within: hmm_bpti/scripts/jupyter_notebooks
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Run hmm_bpti/scripts_final/cleaning.sh
Use the 3 database directories as arguments, as indicated by the script.
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Follow hmm_bpti/scripts/redundancy.sh
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Follow hmm_bpti/scripts/alignment.sh
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Follow hmm_bpti/proteins_2/alignment_shortener.sh
Note: The corresponding Uniprot databases are managed outside the Github repository due to their size.