toolkitbio 1.0.5

A bioinformatics toolkit for DNA sequence analysis, FASTA/GenBank file operations, NCBI queries, sequence alignment, phylogenetics, and protein structure visualization.

🧬 toolkitbio

A comprehensive Python bioinformatics toolkit for DNA sequence analysis, file format conversion, NCBI queries, sequence alignment, phylogenetics, and protein structure visualization.

Installation

pip install toolkitbio

Features

Module	Description
seq_operations	DNA slicing, concatenation, transcription & translation
fasta_reader	Parse and read FASTA files
genbank_writer	Create GenBank format files
fasta_to_genbank	Convert FASTA → GenBank
gene_annotation	Add annotations and features to sequences
ncbi_fetch	Fetch sequences from NCBI Entrez
pairwise_align	Pairwise sequence alignment
muscle_align	Multiple sequence alignment via MUSCLE
phylo_tree	Phylogenetic tree construction (UPGMA/NJ)
pdb_viewer	3D protein structure visualization

Quick Start (Python API)

from toolkitbio import dna_operations, read_fasta, fetch_from_ncbi

# DNA operations
result = dna_operations("ATGCTAGCTAGCTAGCTG", start=3, end=11)
print(result["rna"])       # RNA sequence
print(result["protein"])   # Protein sequence

# Read FASTA file
records = read_fasta("sequences.fasta")

# Fetch from NCBI
data = fetch_from_ncbi("NM_001301717")
print(data["organism"], data["length"])

Command-Line Interface

# DNA sequence operations
toolkitbio seq-ops --seq ATGCTAGCTAGCTAGCTG

# Read FASTA file
toolkitbio read-fasta sequences.fasta

# Fetch from NCBI
toolkitbio fetch-ncbi NM_001301717

# Pairwise alignment
toolkitbio align-pair --seq1 AGTACACTGGT --seq2 AGTACGCTGGT

# Convert FASTA to GenBank
toolkitbio convert input.fasta output.gb

# Build phylogenetic tree
toolkitbio phylo-tree aligned.fasta --method upgma

# View 3D protein structure
toolkitbio view-pdb 1A3N --save structure.png

Requirements

• Python >= 3.8
• Biopython >= 1.80
• Matplotlib >= 3.5
• NumPy >= 1.21
• MUSCLE (optional, for multiple alignment)

License

MIT License - see LICENSE for details.

Author

ravi — [e-mail]