Calculate the coverage of a protein having a list of its peptides
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 ?
Thank you.
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Jean-Karim Heriche
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arronar
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arronar
1 answer
Just use regular expressions to match the peptides to the protein sequence and record an X at each matched position. When all of the peptides have been processed, count the Xs.
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Jean-Karim Heriche
No need to sum anything. Here is a perl way of doing it:
my $cover_seq = $protein_seq; # copy in which we're going to replace matches by X
foreach my $peptide_seq(@peptides) {
if ($protein_seq=~/$peptide_seq/) { # peptide matches the protein
my $start = $-[0]; # start position of match
my $end = $+[0]; # end position of match
my $len = $end - $start; # length of the match
# Replace peptide by Xs in protein sequence
substr($cover_seq, $start, $len) = 'X' x $len;
}
}
# Count number of Xs to get coverage
my $coverage = ($cover_seq=~tr/X//)/length($cover_seq) * 100;
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While this is not a R solution, have you thought of doing multiple-sequence alignment?
I tried clustal omega but I don't know how to get its results inside R and also it doesn't seem to return a percentage of coverage.
Not my field of work, however I found 2 solutions looking in google. Not tested my end. Try and see if it fits yours.
For MS data : isobar R package does the work, check the pdf
I also found this tool Protein Coverage Summarizer but it's not an R package
Thank you but none of them seem to can help me.