This repository contains a number of python scripts and sqlite3 databases for determining statistics on known protein epitopes.
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.DS_Store
AA_and_SS_Percentages.csv
ANTIJEN.csv
Analyzed DB Stats.xlsx
AntiJen epitopes with structures.xlsx
EPIMHC.csv
EPITOPES.sqlite
EpiMHC epitopes with structures and mini-analysis.xlsx
IEDB epitopes with structures.xlsx
IEDB.csv
MHCPEP.csv
README.md
SYFPEITHI.csv
db_analyzer.py
db_combiner.py
db_pattern_analyzer.py
db_regex_analyzer.py
epitope_wrangler.py
iedb_nonbinders.csv
iedb_nonbinders.xlsx

README.md

#immunogenicity-db-analysis

The files in this directory are being used as part of a project to determine statistics on the space of known immunogenic regions in proteins with known structures.

XLSX files:

Initial reformats of various databases of experimentally-determined epitope sequences in proteins.

.py files:

Various scripts for analyzing sqlite3 databases of large numbers of peptide sequences. In particular, db_regex_analyzer.py will determine statistics on epitopes whose string of secondary structure codes (DSSP) match a given regular expression input.

EPITOPES.sqlite:

The master database of experimentally-validated epitope sequences, secondary structure strings, PDB acession codes, and parent protein sequences.