https://github.com/fangfufu/amplifyp

Python rewrite of William Engels's Amplify4
https://github.com/fangfufu/amplifyp

Last synced: 6 months ago
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Python rewrite of William Engels's Amplify4

• Host: GitHub
• URL: https://github.com/fangfufu/amplifyp
• Owner: fangfufu
• License: gpl-3.0
• Created: 2022-12-05T01:22:43.000Z (almost 3 years ago)
• Default Branch: master
• Last Pushed: 2025-03-24T21:02:13.000Z (7 months ago)
• Last Synced: 2025-03-24T22:20:00.949Z (7 months ago)
• Language: Python
• Size: 777 KB
• Stars: 0
• Watchers: 2
• Forks: 1
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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# AmplifyP

Python rewrite of  William Engels's

[Amplify4](https://github.com/wrengels/Amplify4) by two people who went to

Pembroke College Cambridge, hence AmplifyP.

This is pretty much a work in progress.

## How does it all work?

These are all notes for Fufu to understand.

### Replication configuration

A replication configuration (**Repliconf**) consists of a long strand

of DNA which acts as the **template**, and a **primer**.

The **search()** function enumerates all the possible replication origins, and

calculate the primability and stability score. For a potential replication

origin, if the primability and stability scores are above the threshold, the

index (location) of this potential replication origin is considered as valid.

It is recorded in **origin_idx.fwd** and **origin_idx.rev**. Note that during

the search, the template sequence is searched in both forward and reverse

direction. The process of search in the reverse direction involves reversing

the DNA template. (I will add more information about the reverse compliment

later.)

## Running the unit tests

Please invoke ``pytest`` at the root of the repository.