Protein_tools is a tool for basic analysis of protein and polypeptide sequenses. Using this tool you can estimate sequence length, charge, aminoacid compound and mass of the protein, find out the aliphatic index and see if the protein could be cleaved by trypsin.
If you want to use the Protein_tools, use git clone to this repo. To run this tool, you can use this command:
run_protein_tools('<sequence>', '<procedure>'), where <sequence> is the protein sequence (or several sequences) that should be analysed, and <procedure> is the name of option that you want to be done with the sequence(-s). Please write the name of option and sequences in quotes separated by commas, use only one option per time and make sure that your sequences contain the one-letter names of aminoacids (the case is not important).
-
count_seq_length: counts the length of protein sequence and output the number of aminoacids. -
classify_aminoacids: classify all aminoacids from the input sequence in accordance with the 'AA_ALPHABET' classification. If aminoacid is not included in this list, it should be classified as 'Unusual'.AA_ALPHABET classification:
Class Aminoacids Nonpolar G, A, V, I, L, P Polar uncharged S, T, C, M, N, Q Aromatic F, W, Y Polar with negative charge D, E Polar with positive charge K, R, H -
check_unusual_aminoacids: checks the composition of aminoacids and return the list of unusual aminoacids if they present in the sequence. We call the aminoacid unusual when it does not belong to the list of proteinogenic aminoacids (see AA_ALPHABET classification). -
count_charge: counts the charge of the protein by the subtraction between the number of positively and negatively charged aminoacids. -
count_protein_mass: calculates mass of all aminoacids of input sequence in g/mol or kDa scale. -
count_aliphatic_index: calculates aliphatic index - relative proportion of aliphatic aminoacids in input peptide. The higher aliphatic index the higher thermostability of peptide. -
count_trypsin_sites: counts number of valid trypsin cleavable sites: Arginine/any aminoacid and Lysine/any. aminoacid (except Proline). If peptide has not any trypsin cleavable sites, it will return zero.
An illustration of the capabilities of Protein_tools using a random protein sequence is presented below: sequence: CVWGWAMGEACPNPIKINISAYAKTWYQNGPIGRCCCWVGYTAIRFPHQEMQQNTRFNKP
| Option | Output |
|---|---|
| count_seq_length | 60 |
| classify_aminoacids | 'Nonpolar': 22, 'Polar uncharged': 20, 'Aromatic': 9, 'Polar with negative charge': 2, 'Polar with positive charge': 7, 'Unusual': 0 |
| check_unusual_aminoacids | This sequence contains only proteinogenic aminoacids. |
| count_charge | 5 |
| count_protein_mass | 6918.99 |
| count_aliphatic_index | 0.5049999999999999 |
| count_trypsin_sites | 5 |
Protein_tools has several limitations that can raise the errors in the work of the program. Here are some of them:
- Protein_Tools works only with protein sequences that contains letters of Latin alphabet (the case is not important); also every aminoacid should be coded by one letter. If there are other symbols in the sequence, the tool raise
ValueError"One of these sequences is not protein sequence or does not match the rools of input. Please select another sequence.". In this case you should check if there are punctuation marks, spaces or some other symbols in your sequence. - Be careful to work only with the sequences that contain aminoacids that coded with one letter. If your sequense is "SerMetAlaGly", Protein_tools reads it as "SERMETALAGLY".
- The list of available functions is available in section "Options". If you see ValueError "This procedure is not available. Please choose another procedure.", probably your spelling of the name of function is incorrect. Please check the name of chosen prosedure and make sure that it is available in the Protein_Tools.
- Shtompel Anastasia (Telegram: @Aenye) — teamlead, developer (options 'count_protein_mass', 'count_aliphatic_index', 'count_trypsin_sites')
- Chevokina Elizaveta (Telegram: @lzchv) — developer (options 'count_seq_length', 'classify_aminoacids', 'check_unusual_aminoacids', 'count_charge'), author of README file