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Compare epitope homology

Project Description

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# Topeology

Topeology compares neoepitope sequences with epitopes from [IEDB](

This software is not currently ready for production use.

## Example

From the command line:

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

In Python:

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

Input looks like:

sample | epitope
—— | ——-

Output looks like:

sample | epitope | iedb_epitope | score
—— | ——- | ———— | —–

## Installation

You can install topeology using [pip](

`sh pip install topeology `

## 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:

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File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
topeology-0.0.3.tar.gz (9.0 kB) Copy SHA256 Checksum SHA256 Source Jan 29, 2016

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