Advanced Sequence Operations

Beyond the basics (transcribe, translate, reverse complement), Seq supports frame-specific translation, restriction analysis, and simple statistics - the operations that come up constantly when preparing sequences for analysis.

Translating in Frames

from Bio.Seq import Seq

dna = Seq("ATGCGTACGTAA")
print(dna.translate())                 # frame 0
print(dna.translate(table=11))         # bacterial table
print(dna.translate(to_stop=True))     # stop at first stop codon

# frames on a longer sequence:
long_dna = Seq("ATGGCTAGTACCGGTA")
for frame in range(3):
    sub = long_dna[frame:]
    prot = sub.translate(table=11, cds=False)
    print(frame, str(prot))

CDS Translation

# cds=True assumes the sequence is a complete coding sequence
# (starts with a start codon, ends with a stop codon)
print(long_dna.translate(cds=True))

GC Content and Statistics

dna = Seq("ATGCGTACGTAACGG")
gc = (dna.count("G") + dna.count("C")) / len(dna)
print(f"GC: {gc:.2%}")

# codon usage quick view
from collections import Counter
codons = Counter(dna[i:i+3] for i in range(0, len(dna) - 2, 3))
print(codons.most_common(5))

Restriction Enzymes (Restriction module)

from Bio.Restriction import RestrictionEnvelope, complete

# list enzymes and find cut sites
from Bio import Restriction
enz = Restriction["EcoRI"]
seq = Seq("AATTGGCCATTAATT")
print(enz.search(seq))  # cut positions

Quality Trimming Concepts (FASTQ)

For NGS reads, common preprocessing is quality trimming: drop leading/trailing bases below a Phred threshold. Biopython exposes quality via letter_annotations["phred_quality"]; a simple trimmer:

def trim_qual(rec, q_min=20):
    q = rec.letter_annotations.get("phred_quality", "")
    if not q:
        return rec
    left, right = 0, len(q)
    while left < right and q[left] < q_min:
        left += 1
    while right > left and q[right - 1] < q_min:
        right -= 1
    sliced = rec[left:right]
    return sliced

# apply to each record from SeqIO.parse("reads.fastq", "fastq")

Summary

Advanced Seq operations include frame-specific and CDS-aware translation with genetic tables, GC-content and codon statistics, restriction enzyme site search via Bio.Restriction, and quality trimming of FASTQ records using phred_quality. These turn raw sequences into analysis-ready data.