ProPAS: Protein Property Analysis Software


    ProPAS is used to calculate the basic property of peptides/proteins. The properties include the Isoelectric point (pI), Mass weight (MW) and Hydrophobicity (Hy). Additionally, amino acid composition of all peptides/proteins in the list was also calculated.

There are three options for the input data:
    1. Fasta format: it is the most popular format for protein sequences. Each protein is started with ˇ®>ˇŻ symbol, followed by the sequence name and the comment (separated by the space or table key). And then the sequence was showed in the following line.
    2. Single plain sequence: only contain one protein sequence.
    3. Peptide list: list multiple peptide sequences, one peptide one line, without any other symbols or sequence names and so on.

For the data input, you can paste the data to the text box directly, or load the file from ˇ°File openˇ­ˇ± below the text box. If both of them above contain data/file, the pasted data would be ignored and the file would be used for the calculation.

The results could be exported to the file (ˇ°Save to file:ˇ± in the left bottom) or the right text box. If the output file directory and name were provided, the results would only be exported to the file but not the right text box.

In the ˇ°Parameterˇ± section, you can determine which parameter would be calculated and statistic with special range and step.

The ˇ°Runˇ± button is in the right bottom which will start the calculation. If the result is showed in the right text box, you can click ˇ°save to fileˇ­ˇ± in the bottom to save the results to the file, or click ˇ°Copy to clipboardˇ± to save it in clipboard.

The detail description is as below:

1. Input formats

You can use different formats for input protein/peptide sequences. There are three different formats:

    a. Fasta.
     It is a common format for protein sequences. For each protein sequence, there is a ">" symbol following

    b. Single plain sequence.
     Protein sequence from only one protein.

    c. Peptide list.
     Peptide sequence list. One peptide sequence for each line.

2. Input frame

You can paste the protein/peptide sequence needed to be processed to the frame.

3. Input file and its directory

The file and its directory could be put in the box or selected using "File open...". The 2 and 3 are two different input

4. Properties needed to be analyzed

There are four properties that could be analyzed: Isoelectric point (pI), Mass weight (MW), Hydrophobicity (Hy) and amino acid composition. If you only need to analyze some of them, de-select others.

5. Stat

For pI, MW and Hy, the program could calculate the distribution of protein numbers along the values. If you do not need the distribution, de-select them.

6. Range and step for the distribution

The range to calculate the distribution could be changed in the "from" and "to" box. The "step" is the window size for the calculation.

7. Save the results

The file and its directory to save the results could be put in the box or selected using "Browser".

8. Output frame

If the file and its directory are absent in the box (7), the result would be showed in the output frame.

9. Run button

Click "Run" button to run the program for the calculation.

10. Save button

Click "Save to file..." button to save the results showed in output frame (8) to the file.

11. Copy to clipboard button

Click "Copy to clipboard" button to save the results showed in the output frame (8) to the clipboard, which could be pasted to excel and so on.



Example 1: analyze the protein sequences with fasta format

Example 2: analyze one protein with plain sequence format

Example 3: analyze peptide sequences with peptide list format


The software could be download from the link of ProPAS or the new command line version, and it need the support of ActivePerl.

Detail information could be found in

Any questions or problems, please contact: