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Motif Search

Find patterns and motifs in biological sequences using Biopython and regex.

Required Imports

python
from Bio.Seq import Seq
from Bio import motifs
import re

Core Methods

find() - First Occurrence

python
seq = Seq('ATGCGAATTCGATCGAATTCGATC')
pos = seq.find('GAATTC')  # Returns 4 (first position)

Returns -1 if not found.

count() - Count Occurrences

python
seq = Seq('ATGCGAATTCGATCGAATTCGATC')
n = seq.count('GAATTC')  # Returns 2

find() with Start Position

python
seq = Seq('ATGCGAATTCGATCGAATTCGATC')
first = seq.find('GAATTC')        # 4
second = seq.find('GAATTC', 5)    # 14 (search from position 5)

Code Patterns

Find All Occurrences

python
def find_all(seq, pattern):
    pattern = str(pattern)
    seq_str = str(seq)
    positions = []
    pos = seq_str.find(pattern)
    while pos != -1:
        positions.append(pos)
        pos = seq_str.find(pattern, pos + 1)
    return positions

seq = Seq('ATGCGAATTCGATCGAATTCGATC')
positions = find_all(seq, 'GAATTC')  # [4, 14]

Search Both Strands

python
def find_both_strands(seq, pattern):
    results = []
    for pos in find_all(seq, pattern):
        results.append(('+', pos))
    rc = seq.reverse_complement()
    for pos in find_all(rc, pattern):
        results.append(('-', len(seq) - pos - len(pattern)))
    return results

Regex Pattern Search

For ambiguous or flexible patterns:

python
def regex_search(seq, pattern):
    seq_str = str(seq)
    return [(m.start(), m.group()) for m in re.finditer(pattern, seq_str)]

# Find all ATG start codons
matches = regex_search(seq, 'ATG')

# Find TATA box variants (TATAAA with possible variations)
matches = regex_search(seq, 'TATA[AT]A[AT]')

IUPAC Ambiguity Pattern

python
IUPAC_DNA = {
    'R': '[AG]', 'Y': '[CT]', 'S': '[GC]', 'W': '[AT]',
    'K': '[GT]', 'M': '[AC]', 'B': '[CGT]', 'D': '[AGT]',
    'H': '[ACT]', 'V': '[ACG]', 'N': '[ACGT]'
}

def iupac_to_regex(pattern):
    regex = ''
    for char in pattern:
        regex += IUPAC_DNA.get(char, char)
    return regex

# Search for pattern with ambiguous bases
pattern = 'GATNNTC'  # N = any base
regex = iupac_to_regex(pattern)  # 'GAT[ACGT][ACGT]TC'
matches = regex_search(seq, regex)

Find ORFs (Start to Stop)

python
def find_orfs(seq, start='ATG', stops=['TAA', 'TAG', 'TGA'], min_length=30):
    seq_str = str(seq)
    orfs = []
    start_positions = find_all(seq, start)
    for start_pos in start_positions:
        for frame_offset in range(3):
            if (start_pos - frame_offset) % 3 == 0:
                for stop in stops:
                    stop_pos = start_pos + 3
                    while stop_pos <= len(seq) - 3:
                        codon = seq_str[stop_pos:stop_pos + 3]
                        if codon == stop:
                            if stop_pos - start_pos >= min_length:
                                orfs.append((start_pos, stop_pos + 3, seq[start_pos:stop_pos + 3]))
                            break
                        stop_pos += 3
                break
    return orfs

Find Repeats

python
def find_tandem_repeats(seq, unit_length, min_copies=2):
    seq_str = str(seq)
    repeats = []
    for i in range(len(seq) - unit_length * min_copies + 1):
        unit = seq_str[i:i + unit_length]
        copies = 1
        pos = i + unit_length
        while pos <= len(seq) - unit_length and seq_str[pos:pos + unit_length] == unit:
            copies += 1
            pos += unit_length
        if copies >= min_copies:
            repeats.append((i, unit, copies))
    return repeats

seq = Seq('ATGCAGCAGCAGCAGTTT')
repeats = find_tandem_repeats(seq, 3, 2)  # Find CAG repeats

Bio.motifs Module

Create Motif from Instances

python
from Bio import motifs
from Bio.Seq import Seq

instances = [Seq('TACAA'), Seq('TACGA'), Seq('TACTA'), Seq('TGCAA')]
m = motifs.create(instances)

Motif Properties

python
# Consensus sequences
m.consensus              # Most common base at each position
m.degenerate_consensus   # IUPAC degenerate consensus
m.anticonsensus          # Least likely sequence

# Counts and matrices
m.counts                 # Position frequency matrix (counts)
pwm = m.counts.normalize(pseudocounts=0.5)  # Position weight matrix
pssm = pwm.log_odds()    # Position-specific scoring matrix

Information Content

python
# Per-position information content
pwm = m.counts.normalize(pseudocounts=0.5)
pssm = pwm.log_odds()

# Mean information content (bits)
mean_ic = pssm.mean()

# Score range
max_score = pssm.max
min_score = pssm.min

# Relative entropy
print(f'Mean IC: {mean_ic:.3f} bits')
print(f'Max score: {max_score:.3f}')
print(f'Min score: {min_score:.3f}')

PSSM Search

python
seq = Seq('ATGCTACAAGCTACGATACTA')

# Search with threshold
for position, score in pssm.search(seq, threshold=3.0):
    match = seq[position:position + len(m.consensus)]
    print(f'Position {position}: {match} (score: {score:.2f})')

# Search both strands
for position, score in pssm.search(seq, threshold=3.0, both=True):
    print(f'Position {position}: score {score:.2f}')

Calculate Threshold from Distribution

python
# Calculate score distribution from PSSM
sd = pssm.distribution()

# Get threshold for specific false positive rate
threshold = sd.threshold_fpr(0.01)  # 1% FPR

# Get threshold for specific false negative rate
threshold = sd.threshold_fnr(0.1)   # 10% FNR

# Balanced threshold
threshold = sd.threshold_balanced(1000)  # For sequence of length 1000

Reading Motif Files

JASPAR Format

python
from Bio import motifs

with open('motif.jaspar') as f:
    m = motifs.read(f, 'jaspar')
print(f'Name: {m.name}')
print(f'Matrix ID: {m.matrix_id}')
print(m.counts)

MEME Format

python
with open('meme.txt') as f:
    record = motifs.parse(f, 'meme')
for m in record:
    print(f'{m.name}: {m.consensus}')

TRANSFAC Format

python
with open('motif.transfac') as f:
    record = motifs.parse(f, 'transfac')
for m in record:
    print(f'{m.name}: {m.consensus}')

Write Motifs

python
# Write to JASPAR format
with open('output.jaspar', 'w') as f:
    f.write(m.format('jaspar'))

# Write to TRANSFAC format
with open('output.transfac', 'w') as f:
    f.write(m.format('transfac'))

Common Motif Patterns

| Motif | Pattern | Description | |-------|---------|-------------| | Start codon | ATG | Translation initiation | | Stop codons | TAA\|TAG\|TGA | Translation termination | | Kozak | [AG]CCATGG | Eukaryotic translation initiation | | TATA box | TATA[AT]A[AT] | Promoter element | | GC box | GGGCGG | Promoter element (Sp1) | | CAAT box | CCAAT | Promoter element | | Poly-A signal | AATAAA | mRNA polyadenylation | | E-box | CA[ACGT]{2}TG | bHLH TF binding | | CpG island | High CG density | Promoter regions |

Common Errors

| Error | Cause | Solution | |-------|-------|----------| | No matches found | Case mismatch | Use .upper() on both | | Missing matches | Pattern on opposite strand | Search reverse complement too | | TypeError | Mixing Seq and string | Use str() conversion | | ValueError parsing motif | Wrong format specified | Check file format |

Decision Tree

Need to find patterns in sequence?
├── Exact match?
│   ├── Just need position of first? → seq.find()
│   ├── Need count? → seq.count()
│   └── Need all positions? → loop with find()
├── Fuzzy/ambiguous pattern?
│   └── Use regex with re.finditer()
├── IUPAC pattern?
│   └── Convert to regex, then search
├── Both strands?
│   └── Search original and reverse_complement
├── Probabilistic (PWM/PSSM)?
│   └── Use Bio.motifs
│       ├── Create from instances → motifs.create()
│       ├── Read from file → motifs.read() / parse()
│       ├── Get consensus → m.consensus, m.degenerate_consensus
│       ├── Search sequence → pssm.search()
│       └── Calculate threshold → distribution.threshold_fpr()
└── Restriction sites?
    └── Use restriction-analysis skill (Bio.Restriction)

Related Skills

• seq-objects - Create Seq objects for searching
• reverse-complement - Search both strands for motifs
• sequence-io/filter-sequences - Filter sequences that contain specific motifs
• restriction-analysis/restriction-sites - For restriction enzyme site searching
• database-access - Download motif databases from NCBI/JASPAR

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