Atom Biology General Molecule Reaction Tools Trial Virus

Create Motif With Biopython Bio.motifs Module

Q

How to Create Motif With Biopython Bio.motifs Module?

✍: FYIcenter.com

A

Biopython Bio.motifs Module allows you to create a motif object with a list of DNA or protein sequences. A motif object actually represents a sample set of sequences that matches a sequence motif pattern.

1. Create a motif object with a single sequence that matches the motif pattern of "TACAA". 

fyicenter$ python
>>> from Bio import motifs

>>> m = motifs.create(["TACAA"])
>>> len(m)
5

>>> print(m)
TACAA

2. Create a motif object with 7 sequences that matches the motif pattern of "[AT]A[CT][ACG][AC]". 

>>> samples = [
...     "TACAA",
...     "TACGC",
...     "TACAC",
...     "TACCC",
...     "AACCC",
...     "AATGC",
...     "AATGC"
... ]

>>> m = motifs.create(samples)

>>> len(m)
5

>>> print(m)
TACAA
TACGC
TACAC
TACCC
AACCC
AATGC
AATGC

 

⇒ Motif Counts and Consensus with Bio.motifs

⇐ What Is Sequence Motif Analysis

⇑ Biopython for Sequence Motif Analysis

⇑⇑ OBF (Open Bioinformatics Foundation) Tools

2023-07-11, 1503🔥, 0💬

Atom Biology General Molecule Reaction Tools Trial Virus