Simple bioinformatics calculations on specific protein sequences
When working with proteins you often need to make simple bioinformatics calculations on a specific protein sequence.
What is the molecular weight of bovine serum albumin (BSA)?
How many N-glycosylation sites are present in my protein?
What peptides does trypsin cleavage generate?
What is the amino acid composition in my protein?
Questions like these are typical. Therefore, Alphalyse launched GPMAW lite bioinformatics tool to quickly make these calculations.
There are three different ways to enter a sequence into GPMAW lite;
1. Either enter the known accession number from either NCBI or UNIPROT. The sequence will be retrieved into the sequence window automatically. With the NCBI and UniProt lookup function, you can easily find the accession number for any known protein from any organism.
2. Alternatively, paste the sequence directly into the sequence window.
3. Or, you can just type in the sequence using one letter AA code.
GPMAW lite functions
The cleanup function is useful, if your sequence contains numbers. It also works with spaces or lower case letters. When the protein sequence has been entered, you can perform a number of different bioinformatics analyses. First, select the analysis you would like to have performed. Next, click Calculate.
The name and the sequence of the protein is shown at the top of the analysis results. In addition, you can use the Colorize function to highlight specific amino acids residues and potential N-glycosylations sites.
The Protein Information table provides all the basic information about your protein. These include Molecular Weight (mono-isotopic and average mass of non-reduced protein), theoretic calculated molar absorbance and extinction coefficient. It also shows the isoelectric point, and hydrophobicity index.
The Amino Acid Composition function shows an amino acid composition table. It includes numbers and percentage of individual amino acids. If the sequence contains any unusual amino acids it will also be visible in this table.
The protease Digest lists all peptides formed by theoretical complete digestion using the chosen protease. The table contains info about the peptide sequence, and MH+ (mono-isotopic molecular weight of the protonated peptide in reduced form). You will also see the isoelectric point pI and expected retention time in a HPLC run (reversed phase) for each peptide. It is possible to sort all columns. You do so by clicking the header of the column. The columns can thus show peptides by position, HPLC retention time or by mass.
In conclusion, GPMAW lite is an online software for simple and easy bioinformatics calculations on protein amino acid sequences.
You can access GPMAW lite for free from any browser and computer, smartphone or tablet at our website.