Sequence-enriched region proteins finder

The "Select from Organism" option retrieves protein sequences from UniProt across various species, defaulting to human. Custom FASTA sequences can also be uploaded. Point denotes a key parameter pair: (18, 20) requires at least 18 target residues within any 20-residue window; (30, 50) requires at least 30 within any 50-residue window. We recommend an initial coarse screening using fixed-mode parameters, followed by exhaustive retrieval via formula-mode. Retrieved results are displayed immediately; non-retrieved entries require 3–5 seconds in formula mode (mutant datasets may take ~5 minutes).

Example result

Pattern

Pattern (Task Word):

Pattern Syntax:

D-E: Matches D or E at the position.
DE: Matches the exact dipeptide "DE".
.D: Matches any residue followed by D.

Sequence Input

Enter Manually

Upload FASTA (• .fasta, .fa • ≤2MB • Auto-deleted in 12h)

Select from Organism

Scanning Window Settings

Start Window

End Window

Step Size

Analysis Mode

Fixed Mode (Target mode) – Specify exact (hit, window) pairs

Formula Mode (Scan mode) – Use two reference points to derive dynamic window size

Score Mode (Smith-Waterman) – Use a scoring threshold

Proportion Mode (Rate mode) – Use a proportion threshold for analysis

Formula Mode: Reference Points

Define two data points (Hit Count, Window Size) to calculate scanning window dynamically.

Point 1

Hit Count:

Window Size:

Point 2

Hit Count:

Window Size:

Fixed Mode

Enter comma-separated hit/window pairs: hit1,window1,hit2,window2,...

Fixed Points:

Score Mode

Score Threshold: Sequences with score ≥ threshold will be reported (should not be lower than 10).

Proportion Mode

Proportion Threshold: Sequences with proportion ≥ threshold will be reported (range: 0.0 to 1.0).

Analyzing... Please wait.