Figure 1

Proteogenomic Mapping Pipeline Windows GUI. The proteogenomic mapping pipeline requires three files from the user and offers several options. a. First, the user must provide a FASTA formatted file specifying the proteins for which to search. b. The user also supplies a FASTA formatted file specifying the genome in which to search for the peptides. The file can contain the entire genome as one large entry or multiple entries containing only selected features of interest. For example, the file may contain all exons for an organism. c. The user then selects an output file. Two files will be created. The file selected by the user will contain detailed information about the mapping. An additional FASTA file, with ".fasta" appended the name as the file selected by the user, contains the ePST sequence in FASTA format. d. The user can select to ignore splice sites or to use canonical splice sites when searching upstream for the start of the ePST sequence and downstream for the stop of the sequence. e. A genetic code table file, which specifies the mapping from codons to amino acids as well as start and stop codons, must also be provided. f. Because the code table file can contain multiple mappings, the desired mapping must be selected.