FASTG to Protein Library

This package generates a candidate protein library in two phases:

1. Parsing a FASTG file to create graph traversals of longer stretches of DNA

   • FASTG is parsed into a directed graph. A depth-first search is made on all connecting edges. The DFS traversal is then used to concatenate all DNA sequences in the path.
   • DNA sequences are translated to mRNA and split into candidate proteins at the stop codon. Each DFS traversal can, and will, produce a set of candidate protein sequences.
   • Protein sequences are filtered on length and amino acid redundancy.
   • Protein sequences are cleaved into peptide sequences.
   • DFS traversals, proteins and peptides are stored in a SQLite database. The linking relationship between all three is maintained in the DB.
   • A FASTA file of peptides is produced for the user. This FASTA file is to be used in a search against MSMS data.

2. Using verified peptides as a filter to produce a final candidate peptide library

   • The user will invoke the code with
     • DB
     • list of peptide sequences or peptide FASTA
     • It is expected that the submitted peptides have been verified against MSMS and they represent found and identified peptide sequences
   • The verified peptides are used to filter proteins from the database, these proteins become the final library.
   • The verified peptides are used to score the proteins for
     • coverage
     • percent of verified v. total peptide association
   • Final user output
     • SQLite database
     • Protein score text file, comma delimited
     • Filtered protein FASTA file