Skip to main content
Borzoi Chromatin Accessibility MORSE
License: Borzoi uses Apache-2.0 for code and CC-BY-4.0 for model weights and may require explicit attribution when utilized. Please refer to the code license and model weights license for full terms.

This constraint is open source. Any third-party models, product names, or trademarks referenced are the property of their respective owners, and Proto is not affiliated with them.

Go to Tool Page
evo-design/proto-language/proto_language/constraint/sequence_annotation/borzoi_chromatin_accessibility_morse_constraint.py
View source
Copy citation
Constraint contributors
Score target proposals against a Borzoi chromatin accessibility MORSE objective.

​
API Reference

ConfigBorzoiChromatinAccessibilityMorseConfig Source
Configuration for Borzoi chromatin accessibility MORSE scoring.
​
enum
default:"human"
Borzoi species head to use: human or mouse.Options: human, mouse
​
string
default:".--. .-. --- - ---"
Morse pattern; use ’.’, ’-’, and spaces between letters.
​
integer
default:"25"
Length of each dot window.
​
integer
default:"75"
Length of each dash window.
​
integer
default:"25"
Gap between symbols within a letter.
​
integer
default:"75"
Gap between letters in the Morse pattern.
​
integer
default:"0"
Target-relative start coordinate where the Morse pattern begins.
​
enum
default:"global_max"
Scale signal by full-output max, target-region max, or not at all.Options: global_max, region_max, none
​
number
default:"0.0"
Minimum normalized high-minus-low signal margin to reward.
​
number
default:"0.0"
Penalty weight when the normalized contrast margin is too small.
​
number
default:"0.0"
Reward weight for larger raw target signal range.
​
number
default:"0.0"
Reward weight for larger raw signal in dot and dash windows.
​
number
default:"0.0"
Penalty weight for larger raw signal in gap windows.
​
enum
default:"log1p"
Transform for raw amplitude and window-mean reward terms.Options: log1p, identity
​
string
default:"cuda"
CUDA device for Borzoi inference.
​
integer
default:"1"
Candidate sequences per Borzoi model batch.
​
integer
default:"0"
Leading target bases to ignore before accessibility scoring.
​
List[integer]
default:"[1901]"
Borzoi chromatin-accessibility tracks; defaults by organism.
​
enum
default:"mean"
How to combine Borzoi replicate signals.Options: mean, min, std, lcb

​
Usage

python

​
Metadata