Input Sequence

Paste a raw sequence or one or more FASTA sequences. Non-protein characters are stripped automatically. Input limit: 500,000,000 characters.

Window size (aa) Residues to extract

Position (1-based) Anchor position in sequence

Anchor

Output mode

💡 Quick Summary

Window Extractor Protein accepts a protein sequence along with a window size, a position, and an anchor mode (centered on / ending with / starting with). The residues within the window are returned either as a new sequence, as uppercase text within the full sequence, or as lowercase text within the full sequence. Useful for extracting subsequences using position information.

📋 How to Use

Paste a raw protein sequence or one or more FASTA sequences into the input area. Input limit is 500,000,000 characters.
Set the Window size — the number of residues to extract (default 5).
Choose an Anchor: Centered on places the window symmetrically around the position; Ending with makes the position the last residue of the window; Starting with makes the position the first residue of the window.
Set the Position — the 1-based anchor position within the sequence (default 10).
Choose an Output mode: New sequence returns only the window residues as a FASTA entry; Uppercased in context returns the full sequence with the window in uppercase; Lowercased in context returns the full sequence with the window in lowercase.
Click Run. Each input sequence produces one output FASTA entry.
Use the Copy button to copy the result to your clipboard.
Click Load Example to try with a sample 41-residue sequence, window size 5, centered on position 10.

🧮 Formulas & Logic

Centered on position P, window W

start = P − round(W/2) + 1, end = start + W − 1 (1-based, clamped to sequence bounds)

Ending with position P, window W

start = P − W + 1, end = P (1-based, clamped)

Starting with position P, window W

start = P, end = P + W − 1 (1-based, clamped)

📊 Result Interpretation

Sequences Processed

Number of FASTA records successfully processed.

Window Info

The window size, anchor position, and anchor mode used for this run.

🔬 Applications

Extracting a fixed-size neighbourhood around a phosphorylation site, cleavage site, or mutation for motif analysis
Obtaining the sequence context around an active-site residue for structural comparison
Cutting out a defined window for local alignment or scoring matrix calculations
Generating uppercase-highlighted views of a functional domain within its full protein context
Providing input for machine-learning models that require fixed-length peptide windows

⚠️ Common Mistakes & Warnings

Window is clamped at sequence boundaries

If the computed window extends beyond the start or end of the sequence it is automatically clamped. The actual extracted length may therefore be shorter than the requested window size, and this is reflected in the FASTA title of the output.

Non-protein characters are stripped

Any character that is not a valid amino acid letter is removed from the sequence before extraction. Digits, whitespace, and punctuation are all stripped automatically.

Position must be within the sequence

If the anchor position is greater than the sequence length the record is skipped and a warning is shown. Positions start at 1.

❓ Frequently Asked Questions

What is the difference between the three anchor modes?

"Centered on" places the window symmetrically around the given position — for a window of size 5 centered on position 10, residues 8–12 are returned. "Ending with" returns the W residues that finish at the given position. "Starting with" returns the W residues that begin at the given position.

What happens if the window extends past the end of the sequence?

The window is clamped to the sequence boundaries. You will still receive output, but it will be shorter than the requested window size. The FASTA title records the actual start and end positions used.

What is the difference between "New sequence" and the context modes?

"New sequence" returns only the residues within the window as a compact FASTA record. "Uppercased in context" returns the full source sequence in lowercase with the window region in UPPERCASE — useful for seeing where the window sits. "Lowercased in context" does the reverse: the full sequence is uppercase and the window is lowercase.

Can I process multiple sequences at once?

Yes. Paste any number of FASTA-formatted sequences. The same window size, position, anchor, and output settings are applied to every sequence independently.

Why is there no complement strand option?

Protein sequences represent a linear chain of amino acids and have no complementary strand. The complement option is only relevant for DNA/RNA tools.