Hi,

I am trying to implement protein pairwise sequence alignment using "Global Alignment" algorithm by 'Needleman -Wunsch'. I am using VB.NET.

I am not clear about how to include 'Blosum62 Matrix' in my source code to do the scoring or to fill the two-dimensional matrix?

I have googled and found that most people suggested to use flat file which contains the standard 'Blosum62 Matrix'. Does it mean that I need to read from this flat file and fill my coded "Blosum62 Martrix' ?

Also, the other approach could be is to use some mathematical formula and include it in your programming logic to construct 'Blosum62 Matrix'. But not very sure about this option.

Any ideas or insights are appreciated.

Also, is there any pesudo algorithm to do the protein pairwise alignment using Global available? I tired to find the basic steps of the alogrithm online but no luck so I am planning to do the same steps as I did for the global pairwise alignment of Nucleotides

Thanks.

Thanks Istvan for your suggestion. I will work on the same lines.