Motif Finder in FASTA Genomes

This Python script searches for occurrences of a given DNA motif in a FASTA genome file and outputs the results in BED format.

Features

• Search motif occurrences on the forward strand by default.
• Optionally search the reverse complement strand.
• Supports DNA motifs with IUPAC ambiguity codes (e.g. N, V, H, D, B, M, R, W, S, Y, K).
• Outputs BED file with motif locations and matched sequences.
• Supports output compression with .gz extension.
• Progress bar shows processing progress based on total bases for smooth tracking.
• Prints summary of total matches and elapsed runtime.
• Minimal dependencies (biopython required).

Installation

# Python 3.x
pip install biopython tqdm

Usage

python find_motif.py --fasta genome.fa --out motifs.bed --motif GATC

Options

Parameter	Description
--fasta	Input genome FASTA file (required)
--out	Output BED file path (required). Use .gz for gzip output
--motif	Motif sequence with IUPAC codes (required). Examples: GATC, NVH
--reverse	If set, also searches reverse complement strand

IUPAC Ambiguity Codes Supported

Code	Meaning	Bases Included
A	Adenine	A
C	Cytosine	C
G	Guanine	G
T (U)	Thymine (Uracil)	T
N	Any base	A, C, G, T
V	Not T	A, C, G
H	Not G	A, C, T
D	Not C	A, G, T
B	Not A	C, G, T
M	Amino	A, C
R	Purine	A, G
W	Weak	A, T
S	Strong	C, G
Y	Pyrimidine	C, T
K	Keto	G, T

Output BED Format

The output file contains tab-separated columns:

chrom  start  end  name  score  strand  matched_sequence

• start is 0-based coordinate.
• end is non-inclusive.
• name includes motif, chromosome, and match index.
• score is always 0.
• strand is + or -.
• matched_sequence is the actual matched motif sequence from the genome.

Example

Search for motif "GATC" on the plus strand and save compressed output:

python find_motif.py --fasta dm6.fa --out dm6_GATC_motifs.bed.gz --motif GATC

Search for a motif with ambiguity codes on both strands:

python find_motif.py --fasta genome.fa --out motifs.bed --motif NVH --reverse

License

MIT License

Contact

For suggestions or issues, please submit a GitHub issue.