encrypted

Code for cryptide's sequences identification.

Quote:

Santos BPO, Alves ESF, Ferreira CS, Ferreira-Silva A, Góes-Neto A, Verly RM, Lião LM, Oliveira SC, de Magalhães MTQ. Schistocins: Novel antimicrobial peptides encrypted in the Schistosoma mansoni Kunitz Inhibitor SmKI-1. Biochim Biophys Acta Gen Subj. 2021 Nov;1865(11):129989. doi: 10.1016/j.bbagen.2021.129989. Epub 2021 Aug 10. PMID: 34389467.

For usage, python3 is necessary.

Example:

python3 encrypted.py -f fastafile.fasta -t protein -cl 2 -l 500 3000 -act antibacterial -n 1

Decoding the arguments:

• File (-f): a fasta or multifasta file.

• Activity types (-act): in the moment, only antibacterial is available.

• Cleavage types (-cl): 1 for argCproteinase; 2 for trypsinKproteinase; 3 for trypsinRproteinase, 4 and 5 for chymotrypsin, 6 pepsin and 7 for trypsinGKproteinase.

• Length (-l): two enters are necessary, being the first the lower peptides length and the second, the higher length (in Daltons).

• Type (-t): 'protein' or 'peptide'. The first option cleavages the sequence(s) while the second jumps this step.

• Number (-n): a way to separate different predictions. You can type any number.

• Help (-help): print in the screen the information above.

Exit files:

CSV table with predicted peptides and their physicochemical properties;

CSV table with MS/MS peptides fragmentation (mass spectrometry data).

Plotting

If the user wants to visualize the data, a three dimensional plot is additionally available.

• File (-f): a csv file originated by encrypted.py.

• Number of clusters (-cl): kmeans clusterization. User defined number of clusters.

• Output (-o): name of the output file.

Example:

python3 pca_v2.py -f dataframe.csv -cl 3 -o clusters01