Instructions for use - GPMAW lite, the free protein calculation tool
GPMAW lite is a free bioinformatics tool for making simple protein properties calculations. You can use it on any protein amino acid sequence. Alphalyse has developed the software in collaboration with Peter Hoejrup. Hoejrup also developed the complete GPMAW program.
Click to start GPMAW lite now in a new window. Then return to this page for instructions on how to use the free tool.
3 simple steps for using GPMAW lite
1. First, Enter the Sequence
You can use GPMAW lite to find the amino acid sequences for any known protein easily. The tool uses the NCBI and UniProt databases to search for the sequence. First of all, you can write a sequence directly into the tool. Or, if you wish, you can copy the sequence from other programs or documents. Just remember always to use the 1-letter code.
With the CLEAN function, you remove all non-amino acid characters. For instance, numbers, spaces, and special signs from the sequence. It also turns lowercase letters into uppercase.
Use the RESET function to clear all entries.
2. Then Choose your Analysis
Secondly, you can choose from three types of protein sequence analysis:
Protein information. This function provides basic information about the protein:
- Basic molecular weight (like mono-isotopic and average mass, non-reduced form)
- The theoretically calculated molar absorbance and extinction coefficient.
- Hydrophobicity index.
Amino Acid Composition. Use this analysis to show an amino acid composition table.
- It contains numbers and % of individual amino acids.
- In addition, any unusual amino acids in the sequence will be shown in the table.
Protease digest. This analysis shows you a list of peptides. They are formed by complete theoretical digestion using specific proteases.
The table contains info about the following:
- Firstly the peptide sequence of your protein.
Then follows MH+. (Mono-isotopic molecular weight of the protonated peptide in reduced form).
- Finally, the pI and expected retention time in an HPLC run (reverse phase). This is included for each peptide.
You can sort all the columns - just click the column's header.
3. Finally, Analyse the Results
Last, you can enter the protein sequence as an accession number. The protein name and the accession number will appear at the top of the Analysis Results page.
The COLORIZE function highlights specific amino acids. This also includes potential sites for protein N-glycosylation.
Additionally, you can print all of the Analysis Results with the PRINT function. You will find it at the bottom of the page. Afterward, you may include the information in your lab books and project files. Please also reference our site (www.alphalyse.com) if you publish a paper with data from our tool.