📊 EMBOSS Pepstats: Protein Sequence Statistics

EMBOSS Pepstats is a bioinformatics tool used to calculate various physicochemical properties and statistics for a protein sequence. It provides insights into characteristics such as molecular weight, isoelectric point, amino acid composition, and extinction coefficients.

❓ What is EMBOSS Pepstats?

Pepstats analyzes an amino acid sequence and generates a report detailing its key statistical properties. These properties are fundamental for understanding a protein's behavior, stability, and suitability for various experimental procedures.

  • Physicochemical Properties: Calculates molecular weight, isoelectric point, and more.

  • Amino Acid Composition: Reports the frequency of each amino acid.

  • Comprehensive Statistics: Provides a detailed overview of protein characteristics.

🎯 Why Use Pepstats? For Protein Characterization & Experiment Design

EMBOSS Pepstats is indispensable for:

  • 🔍 Protein Characterization: Gaining a quick understanding of a protein's basic physicochemical properties.

  • 🧬 Experimental Planning: Informing decisions for protein purification (e.g., choosing buffer pH based on pI), electrophoresis, or crystallization.

  • 📊 Peptide Design: Calculating properties for synthetic peptides.

  • 📈 Comparative Analysis: Comparing the statistical properties of different protein sequences or variants.

  • 🎯 Quality Control: Verifying expected properties of a protein sequence.

🧑‍💻 How to Use EMBOSS Pepstats on Job Dispatcher: A Step-by-Step Guide

Follow these simple steps to calculate statistics for your protein sequence(s) with Pepstats:

1️⃣ Navigate to the Tool

  1. From the main menu, go to All Tools (or search for "EMBOSS Pepstats").

  2. Click the prominent Use Tool button located next to "EMBOSS Pepstats."

2️⃣ Input Your Protein Sequence

  • Locate the input box (large text area) or the "upload a Sequence File" option.

  • Paste your protein sequence(s) in FASTA format or upload a FASTA file.

    >ProteinA Alpha domain
MKVLWAALLVTFLAGCQAKVEQAV
>ProteinB Beta chain
GSHMLDPQFTNVYQGLRRSGFP
>ProteinC Gamma subunit
ACDEFGHIKLMNPQRSTVWY

  • Important: You can provide a sequence either by typing into the text area OR by uploading a file, but not both simultaneously. Please clear one input to proceed.

3️⃣ Configure Parameters

  • 📝 Title: Provide a descriptive title for your job (e.g., "My Protein Statistics Report").

  • 💡 Sequence Type: (Automatically set to Protein for Pepstats, as it expects protein input).

  • ➕ INCLUDE TERMINI CHARGES (termini): Choose whether to include the charges of the N- and C-termini in the calculation of the isoelectric point.

    • yes - Default
    • no

  • 🔬 USE MONOISOTOPIC WEIGHTS (mono): Choose whether to use monoisotopic atomic weights instead of average atomic weights for molecular weight calculation.

    • no - Default
    • yes

4️⃣ Submit Your Job

  • Once your sequence is entered and parameters are set, click the Submit or Run button.

  • Your job will be dispatched to the EMBL-EBI Web Service. You will be automatically redirected to a Job Status page to monitor its progress.

5️⃣ Interpret Results

  • On the results page, you will find a detailed textual report of the calculated statistics for your protein sequence(s).
  • The report typically includes molecular weight, isoelectric point (pI), amino acid composition, atomic composition, and extinction coefficients.
  • ⭐ Tip: Use the pI value to determine the optimal pH for protein solubility and purification. The amino acid composition can provide clues about the protein's hydrophobicity or charge.

💬 Need Help?

If you run into issues, please visit our Contact Us page for dedicated support. Happy analyzing!