run_protein_tool

run_protein_tool includes a set of commands that perform various operations with protein or peptide sequences of any length. The input sequence(s) must be written using 1-letter amino acid code and can contain any of the following 20 amino acids:

The following functions are implemented:

1. molecular_weight This function takes 1-letter coded protein sequence(s) (string) and calculates molecular weight rounded to integer in g/mol. The function is not case-sensitive. Usage examples:

run_protein_tool('peptide', function='molecular_weight')
799

run_protein_tool('pEpTiDe', function='molecular_weight')
799

2. one_to_three_letter This function takes 1-letter coded protein sequence(s) (string) and returns a 3-letter coded sequence(s) without spaces (string). Usage examples:

run_protein_tool('PEPTIDE', function='one_to_three_letter')
'ProGluProThrIleAspGlu'

run_protein_tool('p', 'peptide', function='one_to_three_letter')
['Pro', 'ProGluProThrIleAspGlu']

3. amino_acid_frequency This function takes 1-letter coded protein sequence(s) (string), calculates frequency for each unique amino acid and creates a dictionary with amino acids as keys and corresponding frequencies as values. Usage example:

run_protein_tool('MADSEQNQEEAGGGEQREH', function='amino_acid_frequency')
{'M': 5.26,
'A': 10.53,
'D': 5.26,
'S': 5.26,
'E': 26.32,
'Q': 15.79,
'N': 5.26,
'G': 15.79,
'R': 5.26,
'H': 5.26}

4. find_motifs This function takes two string arguments: 1-letter coded protein sequence(s) and a motif of interest, where motif is any sequence which occurence will be searched for in the input protein sequence(s). The function returns position(s) of the motif. Usage example:

find_motifs('MADSEQNQEEAGGGEQREH', function='find_motifs', motif='GG')
[12, 13]

Troubleshooting

Please make sure that your input sequence(s) is written using the 1-letter amino acid code as shown in the examples. A sequence containing letters that do not correspond to one of the 20 amino acids from the table above will result in 'Invalid Input' error. Please note that function find_motifs also requires the motif of interest as input after the function name.

Contributors

Elena Smertina implemented check_protein_seq, molecular_weight, one_to_three_letter and run_protein_tool functions;
Natalia Erofeeva implemented amino_acid_frequency and find_motifs functions.