SERtool - SERfilter

Pattern (Task Word) *Example*

Organism

Parameters (Hit, Window)

Description PR (exact "PR"), PR-GR (PR or GR), R.P (R + any + P).

Wildtype-Protein_NMDER: Wild-type protein control for NMD-escaping frameshift variants.
Frameshift-Protein_NMDER: Protein sequences from frameshift mutations that escape NMD.
Wildtype-CDS_NMDER: Wild-type CDS control for NMD-escaping frameshift variants.
Frameshift-CDS_NMDER: CDS sequences of frameshift mutations that escape NMD.

Hit, Window (14,20): Requires at least 14 target residues within a 20-amino acid window.

* Note: The characters on both sides of the "-" should equal length. Only letters, "." and "-" are allowed in Pattern.

Step 1 - Pattern

Pattern (Task Word):

Only letters (A-Z), "." and "-" are allowed.

Step 2 - Sequence Input

Enter FASTA Upload FASTA Select from Organism

📁 Choose FASTA File (≤10MB)

Sequence ID (Optional)

Uploaded sequences are kept for 48 hours. Paste an ID to reuse a previous upload.

Step 3 - Analysis Mode

Fixed Mode – Exact (hit, window) pairs Formula Mode – Dynamic window based on 2 points Score Mode – Smith-Waterman scoring threshold Proportion Mode – Hit rate threshold

Comma-separated (hit, window) pairs:

Use one pair (e.g., 14,20) or multiple: 14,20,30,50,…

Window is fixed. Hit count is adjustable.

Visualization

Point 1 (Hit, Window)

Hit:

Window:

Point 2 (Hit, Window)

Hit:

Window:

Visualization

Score Threshold (≥10)

Visualization

Proportion Threshold (0.5–1.0)

Visualization

Scanning Window Range

Start Window

End Window

Sequence Enrichment Region Filter