Random Protein Regions - TheBiologyBro

Q: What is the difference between "Replace" and "Preserve" mode?

In Replace mode the ranges are the target — those positions become random and the rest stays. In Preserve mode the ranges are protected — those positions stay exactly as they were and everything outside is randomised.

Q: Can I use both ".." and "-" as range separators in the same input?

Yes — 1..10, 20-30 is valid. Both separators are recognised and may be mixed freely.

💡 Quick Summary

Random Protein Regions selects specific positions or ranges within a protein sequence and either replaces those regions with random residues (leaving the rest intact) or preserves those regions and randomises everything else. Random sequences generated this way can serve as controls for evaluating the significance of sequence analysis results.

📋 How to Use

Paste a raw protein sequence or one or more FASTA sequences into the textarea. Input limit: 500,000,000 characters.
Enter the residue positions or ranges of interest. Use .. or - to specify a range and a comma to separate entries — for example: 1, 5, 10..20, 50-60. Positions are 1-based.
Choose the mode: Replace ranges with random residues fills the specified positions with random amino acids and leaves the rest of the sequence unchanged. Preserve ranges keeps the specified positions intact and randomises everything else.
Click Run. Each input sequence is processed independently and output as a FASTA record. Use Copy to copy the plain-text result.

📊 Result Interpretation

Replace ranges mode

Only the residues at the specified positions are changed to random amino acids. The sequence length does not change.

Preserve ranges mode

Every residue that is not covered by a range is replaced with a random amino acid. The specified positions are output unchanged.

Overlapping ranges

Overlapping or duplicate ranges are handled correctly — each residue position is considered once.

Out-of-bounds ranges

Range endpoints are automatically clamped to the actual sequence length. Positions beyond the end of the sequence are silently ignored.

🔬 Applications

Generating negative-control sequences that preserve specific motifs (e.g. an active site or binding domain) while randomising the background
Destroying specific features (signal peptides, transmembrane regions, conserved motifs) within a sequence for in silico experiments
Producing synthetic sequences that retain fixed structural elements while randomising variable regions
Testing pattern-search or alignment tools against partially-randomised protein inputs

⚠️ Common Mistakes & Warnings

Non-protein characters are stripped before processing

Digits, spaces, and any non-IUPAC amino acid characters are removed from the input before ranges are applied. The position numbers you enter refer to the cleaned sequence.

Randomisation uses all 20 standard amino acids

Random positions are replaced with one of the 20 standard amino acids (A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, Y) each with equal probability.

Ranges are 1-based

Position 1 refers to the first residue of the cleaned sequence. If your ranges were derived from a tool that uses 0-based coordinates, add 1 to each boundary.

❓ Frequently Asked Questions

What is the difference between "Replace" and "Preserve" mode?

In Replace mode the ranges are the target — those positions become random and the rest stays. In Preserve mode the ranges are protected — those positions stay exactly as they were and everything outside is randomised.

Can I use both ".." and "-" as range separators in the same input?

Yes — 1..10, 20-30 is valid. Both separators are recognised and may be mixed freely.

Does the output sequence have the same length as the input?

Yes. Only residues are changed; none are inserted or deleted. The output sequence has the same length as the cleaned input sequence.

Can I process multiple FASTA sequences at once?

Yes — paste multiple FASTA records and each is processed independently with the same ranges and mode. The output preserves the original FASTA headers.