Topeology

Topeology compares neoepitope sequences with epitopes from IEDB.

Note: Topeology is no longer being actively maintained.

Example

From the command line:

topeology --input epitopes.csv --epitope-lengths 8 9 10 11 > scores.csv

In Python:

from topeology import compare
output_dataframe = compare('epitopes.csv')

Input looks like:

Output looks like:

Installation

You can install topeology using pip:

pip install topeology

Currently, topeology use seq-align to quickly compare sequences, wrapped in a C extension. It will be installed if seq-align is installed; otherwise, topeology reverts to using another scorer.

To install topeology with this extension:

• Follow seq-align's installation instructions, and then set SEQ_ALIGN_PATH to the installation directory.
• Install topeology via pip. If topeology is already installed, run pip install topeology --upgrade --no-deps --force-reinstall.

Methodology

Topeology uses Smith-Waterman alignment to align each neoepitope with each IEDB epitope of the same length, and returns the resultant epitope-epitope scores. Only position 3 to the penultimate amino acid are considered.

This software uses the following libraries for Smith-Waterman alignment:

• seq-align
• Complete-Striped-Smith-Waterman-Library