Identifying genomic loci that match peptides

Finding the exact places on a genome that a peptide matches to can be a challenging task, especially if the genome is one that is not represented by the original search file. In this recipe, we'll look at mixing in a classic command-line BLAST recipe to find short, nearly precise matches for peptides on a translated genome sequence to various R genomics pipelines by targeting a GRanges object of the BLAST hits.

Getting ready

For this recipe, we'll use the MSnID, dplyr, withR, GenomicRanges, and Biostrings packages and a search engine output file of Escherichia coli-derived spectra, which can be found in the PXD006247.mzXML.mzid file in this book's datasets/ch6 folder...