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Protein Information Tool

This tool takes in a CSV file with protein names, sequences, types (DNA, RNA, or protein input), then generates a CSV file with:

1. Protein Translation Sequence
2. Protein Length
3. Molecular Weight (in g/mol)
4. Extinction Coefficient ( in M^-1 cm^-1)

The optional '-c' will provide generate the file above, plus an additional CSV file with each protein's 20 canonical amino acids breakdown.

Running the script

python Protein_Info.py Sequences.csv [-c]

The input file and script have to be in the same directory.

Example

Input file

Name	Type	Sequence
Protein1	D	ATGACG...TAA
Protein2	RNA	AUGGAU...UAA
Protein3	Protein	MNF...PTV

Output file "Protein_results.csv"

Name	Type	Sequence	Translation	Protein Length	MW (g/mol)	Extinction Coefficent
Protein1	D	ATG...TAA	MTR...PTV*	577	64209.38	35985
Protein2	RNA	AUG...UAA	MDS...DSD*	387	43495.1	31140
Protein3	Protein	MNF...PTV	MNF...PTV	565	62778.78	35985

Output file will generate the file above plus "Protein_AA_Counts.csv" file using optional '-c' command line input

Amino Acid	Protein1	Protein2	Protein3
A	61	20	59
R	41	20	38
N	25	12	25
D	22	23	21
C	3	12	3
Q	39	20	39
E	38	31	36
G	37	16	37
H	9	10	9
I	20	9	20
L	34	33	33
K	40	29	40
M	25	9	24
F	25	10	25
P	40	32	40
S	33	30	33
T	29	35	27
W	2	2	2
Y	14	11	14
V	40	23	40

Requirements

Required dependecies

Dependencies for script:

python 3.2 or above
pandas 2.2.1 or above

The rest are standard Python libraries.

Input File

A sample sheet named "Sample_Sheet.csv" is included if desired.

Input file can be any name but must be a CSV file and contain the following fields within the file:

• Name
  • Column header must be typed exactly Name .
  • Protein or sequence names can be any acceptable text.
• Type
  • Column header must be typed exactly Type.
  • Fields can be: DNA, dna, D, RNA, rna, R, Protein, protein, P.
  • Any other input will cause it to give you an "Invalid type".
• Sequence
  • Column header must be typed exactly Sequence.
  • DNA can contain any base "ATCG" while RNA can contain bases "AUGC".
    • No mixing DNA and RNA bases (e.g. "ATCU" not allowed).
    • No degenerate bases.
    • Does not have to contain start (ATG) or stop codons (TAG, TAA, TGA).
    • Must be Open Reading Frame (ORF) that is divisble by 3.
  • Proteins can contain any 1-letter code for the 20 amino acids as well as the 5 other non-canoncial amino acids:
    • B, J, O, U, X, Z
      • These are counted if "Protein" type is marked in the Type field.
      • They will be used to calculate length and MW, but will not be counted in the optional amino acid counts file.
    • Does not have to end with common stop codon indicators (*, -), though "STOP" is invalid.

For all these fields, please be aware of any leading or trailing white spaces.

Please let me know if there are any bugs or any new science updates requireming me to update the file.