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How to Use EpiPred

The EpiPred server predicts B-cell and T-cell epitopes from protein sequences using an advanced deep learning model with attention mechanisms and bidirectional LSTM networks.

Step 1: Input Your Sequences

EpiPred requires protein sequence(s) in FASTA format and cannot handle nucleic acid sequences.

Option A: Paste Sequences

Paste protein sequence(s) in FASTA format into the text field marked by arrow A.

Option B: Upload File

Upload a FASTA file using the file upload button marked by arrow B.

Step 2: Submit for Analysis

Click the "Predict Epitopes" button (marked by arrow C) when protein sequences are entered. The analysis may take a few minutes depending on the number and length of sequences.

Step 3: View Results

After the server successfully finishes the job, a results page will appear showing:

  • Summary statistics - Total number of sequences analyzed and epitopes found
  • Interactive threshold control - Adjust confidence threshold to filter results
  • Sequence visualization - View sequences with epitope markup
  • Detailed tables - B-cell and T-cell epitopes with confidence scores

FASTA Format Guide

FASTA format is a text-based format for representing protein sequences. Here's what you need to know:

Basic Structure:
>Header_Line_Starting_With_Greater_Than
AMINO_ACID_SEQUENCE_HERE
>Another_Sequence_Header
ANOTHER_AMINO_ACID_SEQUENCE
Rules:
  • Each sequence must start with a header line beginning with '>'
  • Header lines can contain sequence names and descriptions
  • Sequence lines should contain only standard amino acid letters (A-Z)
  • Multiple sequences can be included in a single submission
  • Blank lines are ignored
Example:
>Human_Insulin_A_Chain
GIVEQCCTSICSLYQLENYCN

>Human_Insulin_B_Chain  
FVNQHLCGSHLVEALYLVCGERGFFYTPKT

>Example_Antigen_Protein
MKLLILTCLVAVALARPKHPIKHQGLPQEVLNENLLRFFVAPFPEVFGKEKVNEL
CARFASLIYGKFVRQPQVWLRIQNYSVMDICDEHQGVMVPGVGVPQALQKYNPD

Interpreting Results

Confidence Scores:

Each predicted epitope comes with a confidence score between 0.0 and 1.0:

  • 0.8 - 1.0: High confidence predictions
  • 0.6 - 0.8: Medium confidence predictions
  • 0.5 - 0.6: Lower confidence predictions
  • Below 0.5: Not shown by default (adjust threshold to view)
Sequence Markup:
B B-cell epitope regions
T T-cell epitope regions
. Non-epitope regions
Position Ranges:

Position ranges are given in 1-based indexing (first amino acid is position 1). For example, "15-34" means the epitope spans from the 15th to 34th amino acid.

Quick Tips
Best Practices:
  • Use descriptive sequence names in headers
  • Check sequences for typos before submission
  • Start with high confidence threshold (0.7-0.8)
  • Consider biological context when interpreting results
Common Issues:
  • Missing '>' at start of header lines
  • Non-standard amino acid characters
  • Sequences that are too short (<10 AA)
  • Mixed protein and DNA sequences
Submission Limits
Max sequences: 50 per submission
Max total length: 300,000 amino acids
Min sequence length: 10 amino acids
Max sequence length: 6,000 amino acids
Max file size: 16 MB
Navigation
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