Sequence Motif Match

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

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@article{grant2011fimo,
  title={FIMO: scanning for occurrences of a given motif},
  author={Grant, Charles E. and Bailey, Timothy L. and Noble, William Stafford},
  journal={Bioinformatics},
  volume={27},
  number={7},
  pages={1017--1018},
  year={2011},
  publisher={Oxford University Press},
  doi={10.1093/bioinformatics/btr064}
}

Constraint contributorsdguo8412bviggiano

Score DNA sequences against sequence motifs using MEME.

• Unwanted motifs: Strong matches (low p-values) result in high penalties, encouraging sequences without these binding sites
• Wanted motifs: Strong matches result in low penalties (rewards), while missing wanted motifs result in high penalties
• No motif specification: Any motif matches are penalized (novelty constraint)

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API Reference

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Usage

>>> from proto_language.core import Sequence, SequenceType
>>> promoter_seq = Sequence("ATCGGCGGGATCGTAATATAGCATGC", "dna")
>>> config = SeqMotifConfig(
...     motifs_path="/data/jaspar_vertebrates.meme",
...     wanted=["SP1", "lacI"],
...     aggregation="average",
... )
>>> results = seq_motif_constraint([(promoter_seq,)], config)
>>> print(results[0].score)  # e.g., 0.15
>>> print(results[0].metadata["motif_constraint"]["found"])  # e.g., {"SP1": 1e-8}

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Metadata