biopython / biopython/biopython

Restriction enzyme opt_temp and inact_temp are hard coded

Open
#4,156 13 comments 0 reactions 0 assignees View on GitHub
Dominant language
Python
Stars
5.2k
Forks
1.9k
Avg merge
2d 6h
Merged PRs (30d)
11

Description

### Setup

I am reporting a problem with Biopython version, Python version, and operating
system as follows:

```python
import sys; print(sys.version)
# -> 3.9.10 (main, Apr 1 2022, 15:43:10) [Clang 13.1.6 (clang-1316.0.21.2)]
import platform; print(platform.python_implementation()); print(platform.platform())
# -> Cpython; macOS-12.6-x86_64-i386-64bit
import Bio; print(Bio.__version__)
# -> 1.79
```

### Expected behaviour
Bio.Restriction reports the published values for `inact_temp` and `opt_temp` comparable to the NEB documentation.

### Actual behaviour
Bio.Restriction give 65 and 37 respectively for the values `inact_temp` and `opt_temp` for all restriction enzymes.

### Steps to reproduce
``` python
from Bio.Restriction import BsmFI
print(BsmFI.inact_temp) # -> 65
print(BsmFI.opt_temp) # -> 37
```

BsmFI is listed as having an [optimal temp of 65](https://www.neb.com/tools-and-resources/usage-guidelines/activity-at-37c-for-restriction-enzymes-with-alternate-incubation-temperatures) with an [inactivation temp of 80](https://www.neb.com/products/r0572-bsmfi#Product%20Information_Properties%20&%20Usage)

### Thoughts
I was reading through the generation code for the `Bio.Restriction` module when [this line](https://github.com/biopython/biopython/blob/master/Scripts/Restriction/ranacompiler.py#L183) caught my eye. It apears that for every enzyme, the temperature of inactivation and for optimal function are hard coded to be 65 and 37 (deg C) respectively.

I would expect that this was something that was generated from the REBASE DB, though I haven't been able to identify a resource that contains information regarding temperatures. However, NEB does provide [tables](https://www.neb.com/tools-and-resources/usage-guidelines/activity-at-37c-for-restriction-enzymes-with-alternate-incubation-temperatures) of [related data](https://www.neb.com/tools-and-resources/usage-guidelines/heat-inactivation). Perhaps there is a source that could be automatically scraped?

I'd be happy to supply a PR to that effect if I could be directed to the proper resource to use. Although I may be misunderstanding the use of these fields.

Contributor guide

Open the contributing guide

Assessment

This issue has not been assessed yet.

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.