Tip: Highlight a part of the sequence to see specific stats.
Live Analysis
Length:0
Detected Features:
Analysis Toolkit
Choose a k value between 2 and 12. Lower values (3–4) reveal general composition patterns;
higher values (6–8) identify specific motifs.
BLAST searches are sent to NCBI servers and may take 30–120
seconds depending on sequence length and server load.
Finds regions starting with ATG and ending with a stop codon in all 6 frames.
Scores impact of substitutions and indels on protein coding and splice sites.
Structural Folding Engine
The folding engine provides state-of-the-art predictive accuracy for proteins, ions, glycans, and small molecules. It evaluates binding affinities and identifies complex co-folding patterns.
Molecular Docking (DiffDock)
Dock a small molecule into the currently loaded 3D protein structure. Ensure you have a protein visible in the 3D Viewer first.
Job ID: --
Pending...
The structural engine inference can take **2-5 minutes**. You can continue using other tabs while the job runs in the background.
Predicts donor (GT) and acceptor (AG) sites using consensus PWM scoring.
Calculates CAI and rare codon ratio relative to host bias.
Identify Promoters, RBS, and Terminators across both
strands.
Scores sequence naturalness via k-mer entropy analysis (Evo 2 proxy).
Predicts gene essentiality relative to Evo 2 likelihood
benchmarks.
Screens sequence against regulated pathogen redline motifs
(Select Agents).
Correlate ORFs with upstream promoters and downstream
terminators.
Only matching regions larger than
'Window Size' with at least 'Threshold' matches will be plotted. Improves clarity for large
sequences.
PCR Parameters
If enabled, the algorithm will prefer codons that introduce "hidden" stop codons in alternate
reading frames (+1/-1) to terminate translation in case of ribosomal slippage.
All: Scans every known enzyme. Common: 19 frequently used cloning
enzymes. Custom: Pick specific enzymes from the list.
Gibson Assembly joins fragments with homologous overlaps. Recommended overlap is 20-40 bp with Tm >
60°C.
Golden Gate uses Type IIS enzymes to create seamless junctions. Ensure your fragments don't contain
internal sites for the chosen enzyme.
Structure Modeling Engine Ready
Detected Pockets
Molecular Docking
DiffDock
DiffDock: Blind docking simulation. Enter a ligand SMILES string above to dock it into the current protein.
SAFESeq AI assistant
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Research & Literature
Generate high-dimensional signatures for the active protein sequence.
Supports **Lipinski's Rule of 5** and heuristic ADMET assessment.