Hi Adam, we have a tool specialised in sequence variants and will shortly be releasing a tool for de novo sequencing where the sequence is not known. Sounds like it is the sort of thing you need. http://www.proteinmetrics.com/how-tos/ - and you can ask for a trial software if you wish. I assume you are using mass spec?

A number of softwares can be used: DNASIS MAX, SnapGene, Vector NTI to name a few. We routinely use first two.

Hello Mr. Adam.

A simple way would be to synthesize a method of combinatorial chemistry entire pool of compounds, eg .: an exercise in synthesizing peptides.

The study and comparison of purified peptides by IR, NMR, spectrophotometry, and others, should give us the answer that we have a relationship.

A program comparing these values will accelerate our search for the unknown peptide.

Best wishes

Dear All 

Thanks for suggestions. John it look like potentially interesting for us. In terms of results I was rather thinking about getting a list of proteins with such N-terminal sequence.