BAC-browser

BAC-browser designs nucleotide sequences, visualizes genomic features, and assembles DNA sequences for synthetic genomics research.

Key Features:

• Nucleotide Sequence Generation: Generates nucleotide sequences from amino acid sequences using a codon frequency table for a specific organism.
• Restriction Site Visualization: Visualizes restriction sites within nucleotide sequences.
• GC Composition Analysis: Visualizes GC composition of nucleotide sequences.
• GC Skew Visualization: Visualizes GC skew of nucleotide sequences.
• Secondary Structure Visualization: Visualizes secondary structure of nucleotide sequences.
• Regular Oligonucleotide Fragmentation: Breaks down sequences into oligonucleotides of a certain length.
• Thermodynamic Alignment Fragmentation: Breaks down sequences into oligonucleotides with thermodynamic alignment.

Scientific Applications:

• Synthetic Sequence Design: Supports the design of synthetic nucleotide sequences for synthetic genomics.
• DNA Sequence Assembly: Enables assembly of DNA sequences from synthetic oligonucleotides designed in different modes.

Methodology:

BAC-browser uses codon frequency tables for specific organisms to generate nucleotide sequences from amino acid sequences, and implements regular fragmentation and thermodynamic alignment-based fragmentation for oligonucleotide breakdown.