Hello out there.
I was wondering if there is a simple way using R to calculate the coverage of a protein when you have a list of peptides from it and its initial sequence.
For example let's say that we have this protein sequence taken from uniprot:
MAFSAEDVLKEYDRRRRMEALLLSLYYPNDRKLLDYKEWSPPRVQVECPKAPVEWNNPPS EKGLIVGHFSGIKYKGEKAQASEVDVNKMCCWVSKFKDAMRRYQGIQTCKIPGKVLSDLD AKIKAYNLTVEGVEGFVRYSRVTKQHVAAFLKELRHSKQYENVNLIHYILTDKRVDIQHL EKDLVKDFKALVESAHRMRQGHMINVKYILYQLLKKHGHGPDGPDILTVKTGSKGVLYDD SFRKIYTDLGWKFTPL
and we have a list of some of its peptides that may or may not overlap one an other.
pepts = c("DRRRRMEALLLSLY", "YPNDRKLL", "DYKEWSPPRVQVECPKAPVEWNNPPS EKGLIVGHFSGIKYKGEKAQA", "SEVDVNK", "MCCWVSKFKDAMRRYQGIQ", "TCKIPGK", "VLSDLD AKIKAYNLTVEGVEGFVRYSRVTK", "DRRRRMEALLLSLYYPNDRKLL" , "SEVDVNKMCCWVSKFK")
Can we somehow to calculate the coverage ?