SigmaP: Python package for predicting sigma70 promoter in Escherichia coli K-12
Project description
SigmaP
Python package for Sigma70 promoter Prediction. This package used Sigma70Pred (Patiyal et al. 2022).
Installation
This package can be installed by pip.
pip install sigmap
How to use
First, prepare fasta file containing DNA sequence. Minimum length for prediction is 81nt. Then, calculate probability score by SigmaFactor. Run prediction model by .predict method. Results will be returned as pd.DataFrame.
from sigmap import SigmaFactor
sigma = SigmaFactor()
df_out = sigma.predict('tutorial/example_seq.fa')
| ID | Sequence | Probability Score | Prediction |
|---|---|---|---|
| >Seq_1 | TAGCACGACGATAATATAAACGCAGCAAAAAAAAAAAAAAAAAAAA... | 0.145 | Non-Promoter |
| >Seq_2 | AGCTTGCGTCAATGGGCAAGGTGGGCTTGCATTTGCTTAATAGAAA... | 0.478 | Promoter |
| >Seq_3 | TCGTTTTATTTCTTTTTTCTCCATTGAACTTTCAGTTTCTTTTCTA... | 0.692 | Promoter |
| >Seq_4 | CGCAGCGGGTTTACCCTCTGACCGTTTCTGTTACGAAGGCTTTTTA... | 0.216 | Non-Promoter |
| >Seq_5 | TGCTGCTTGGTCTGTGGGTTGCCGCACAGGTTGCCGGTTCCACCAA... | 0.162 | Non-Promoter |
| >Seq_6 | GAATCCAACTAATGTTGTAAACTGGCAAGGTAATGTCATTAGTCAT... | 0.418 | Promoter |
Contact: Goosang Yu (gsyu93@gmail.com)
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