biological-expert

Biological Sciences Expert

Expert guidance for biology, biotechnology, genetics, bioinformatics, and computational biology applications.

Core Concepts

Molecular Biology

• DNA, RNA, and protein structure
• Central dogma (transcription, translation)
• Gene expression and regulation
• Genetic mutations and variations
• CRISPR and gene editing
• Protein folding and structure

Genomics & Bioinformatics

• DNA sequencing (Sanger, NGS, long-read)
• Genome assembly and annotation
• Sequence alignment (BLAST, BLAT)
• Variant calling and analysis
• RNA-seq analysis
• Phylogenetic analysis

Systems Biology

• Metabolic pathways
• Protein-protein interactions
• Gene regulatory networks
• Mathematical modeling
• Pathway analysis
• Network biology

DNA Sequence Analysis

from Bio import SeqIO, Seq
from Bio.Seq import Seq
from Bio.SeqUtils import gc_fraction, molecular_weight
from typing import Dict, List

class DNAAnalyzer:
    """Analyze DNA sequences"""

    def __init__(self, sequence: str):
        self.sequence = Seq(sequence.upper())

    def basic_stats(self) -> Dict:
        """Calculate basic sequence statistics"""
        return {
            "length": len(self.sequence),
            "gc_content": gc_fraction(self.sequence) * 100,
            "molecular_weight": molecular_weight(self.sequence, "DNA"),
            "nucleotide_counts": self._count_nucleotides()
        }

    def _count_nucleotides(self) -> Dict[str, int]:
        """Count each nucleotide"""
        return {
            'A': self.sequence.count('A'),
            'T': self.sequence.count('T'),
            'G': self.sequence.count('G'),
            'C': self.sequence.count('C')
        }

    def transcribe(self) -> str:
        """Transcribe DNA to RNA"""
        return str(self.sequence.transcribe())

    def translate(self, table: int = 1) -> str:
        """Translate DNA to protein"""
        return str(self.sequence.translate(table=table))

    def reverse_complement(self) -> str:
        """Get reverse complement"""
        return str(self.sequence.reverse_complement())

    def find_orfs(self, min_length: int = 100) -> List[Dict]:
        """Find Open Reading Frames"""
        orfs = []

        for strand, seq in [(+1, self.sequence), (-1, self.sequence.reverse_complement())]:
            for frame in range(3):
                trans = seq[frame:].translate(to_stop=False)

                for i, aa in enumerate(trans):
                    if aa == 'M':  # Start codon
                        for j in range(i + 1, len(trans)):
                            if trans[j] == '*':  # Stop codon
                                orf_len = (j - i) * 3

                                if orf_len >= min_length:
                                    orfs.append({
                                        "strand": strand,
                                        "frame": frame,
                                        "start": i * 3 + frame,
                                        "end": j * 3 + frame,
                                        "length": orf_len,
                                        "protein": str(trans[i:j])
                                    })
                                break

        return orfs

    def find_motif(self, motif: str) -> List[int]:
        """Find motif positions in sequence"""
        positions = []
        motif = motif.upper()

        for i in range(len(self.sequence) - len(motif) + 1):
            if str(self.sequence[i:i+len(motif)]) == motif:
                positions.append(i)

        return positions