I have a 120-concatenated protein sequence in a fasta file. I would like to split by proteins. How can I identify each protein?
The only way I can think is to break the protein apart on methionine residues, blast each amino acid locus and concatenate any locus that does not score a query protein position of '1'. The theory is simple every protein starts with a methionine residue, however there are plenty of M residues within the protein that don't represent the beginning of the gene.
Breaking the protein apart on M would be easy, but then automating and parsing the blast would be fiddly. Obvioulsy you will need to code it and if its a one off would it be worth it?