Puffin Promoter Activity

License: Puffin is licensed under Custom (UTSW Academic Software License) and has restrictions around commercial use and may require explicit attribution when utilized. Please refer to the license for full terms.

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evo-design/proto-language/proto_language/constraint/sequence_annotation/puffin_promoter_activity_constraint.py

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@article{dudnyk2024puffin,
  title={Sequence basis of transcription initiation in the human genome},
  author={Dudnyk, Kseniia and Cai, Donghong and Shi, Chenlai and Xu, Jian and Zhou, Jian},
  journal={Science},
  volume={384},
  number={6694},
  year={2024},
  publisher={American Association for the Advancement of Science},
  doi={10.1126/science.adj0116},
  url={https://www.science.org/doi/10.1126/science.adj0116}
}

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Constraint contributors

Score Puffin promoter signal for target DNA segments.

API Reference

ConfigPuffinPromoterActivityConfig Source

Configuration for Puffin promoter activity scoring.

string

Upstream DNA padding supplied to Puffin.

string

Downstream DNA padding supplied to Puffin.

List[string]

Puffin output channels to average.

array

Optional 0-based half-open interval relative to the target segment.

enum

default:"maximize"

Whether high or low Puffin promoter signal is preferred.Options: maximize, minimize

number

default:"2.0"

Mean activity treated as saturating success.

number

default:"0.2"

Peak fraction treated as saturating success.

number

default:"1.0"

Weight for the activity component.

number

default:"1.0"

Weight for the TSS sharpness component.

PuffinPredictionConfig

Runtime settings for Puffin prediction.

Usage

python

from proto_language.core import Constraint
from proto_language.constraint import puffin_promoter_activity_constraint, PuffinPromoterActivityConfig

constraint = Constraint(
    inputs=[segment],
    function=puffin_promoter_activity_constraint,
    function_config=PuffinPromoterActivityConfig(
        # Configure parameters here
    ),
)

scores = constraint.evaluate()

Metadata

Property	Value
Key	`puffin-promoter-activity`
Function	`puffin_promoter_activity_constraint`
Category	`sequence_annotation`
Mode	`discrete`
Uses GPU	`True`
Supported Types	`dna`

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Puffin Promoter Activity

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