🧬 Genewise: Gene Prediction & Protein Alignment to Genomic DNA

Genewise is a powerful bioinformatics tool used to predict gene structures in genomic DNA by aligning a protein sequence (or a related DNA sequence) to it. It's particularly useful for identifying genes in newly sequenced genomes or refining gene models based on protein evidence.

❓ What is Genewise?

Genewise takes a protein sequence (or a related DNA sequence) and a genomic DNA sequence, then attempts to find the best possible gene prediction in the genomic DNA that would encode that protein. It accounts for introns, exons, and splice sites, providing a detailed alignment that reflects the gene's structure.

  • Gene Structure Prediction: Predicts exon-intron boundaries in genomic DNA.

  • Protein-Guided Alignment: Uses protein sequence homology to guide gene finding.

  • Detailed Output: Provides comprehensive information on gene structure, translation, and alignments.

🎯 Why Use Genewise? For Accurate Gene Annotation

Genewise is an indispensable tool for:

  • 🔍 Gene Discovery: Identifying novel genes in raw genomic sequence data.

  • 🧬 Gene Model Refinement: Improving the accuracy of existing gene annotations by incorporating protein evidence.

  • 📊 Pseudogene Identification: Distinguishing functional genes from pseudogenes.

  • 🎯 Comparative Genomics: Understanding gene evolution and organization by comparing gene structures across species.

  • 📈 Functional Inference: Linking genomic regions to potential protein products and their functions.

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

Follow these simple steps to predict gene structures using Genewise:

1️⃣ Navigate to the Tool

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

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

2️⃣ Input Your Sequences

  • Locate the two input boxes (large text areas labeled "1st Input Sequence" for the protein/related DNA and "2nd Input Sequence" for the genomic DNA) or the corresponding "upload a Sequence File" options.

  • Paste your sequences in FASTA format or upload FASTA files. (For an instance, in Protein)

  • Input Sequence A (1st Input Sequence):

    >seqA
MGDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE
    ```

  • Input Sequence B (2nd Input Sequence):

    >seqB
MGDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAAGFSYTDANKNKGITWGEDTLMEYLENPKKYIPGTKMIFAGIKKKGERADLIAYLKKATNE
    ```

  • Important: For each input, 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 for both sequences.

3️⃣ Configure Parameters

  • 📝 Title: Provide a descriptive title for your job (e.g., "My Gene Prediction Job").

  • 💡 Sequence Type: (Note: Genewise typically expects a protein query against a DNA target, so the sequence type may be fixed or inferred by the tool.)

  • 📊 SHOW PARAMETERS (para): Choose whether to show the parameters in the output.

    • ON
    • OFF - (Default)

  • 📄 PRETTY ASCII (pretty): Output alignment in a pretty ASCII format.

    • ON
    • OFF - (Default)

  • 🧬 GENE STRUCTURE (genes): Output the predicted gene structure.

    • ON
    • OFF - (Default)

  • 🔄 TRANSLATION (trans): Output the translation of the predicted gene.

    • ON
    • OFF - (Default)

  • 📜 CDNA (cdna): Output the cDNA sequence of the predicted gene.

    • ON
    • OFF - (Default)

  • 📝 EMBL FEATURE (embl): Output EMBL feature table.

    • ON
    • OFF - (Default)

  • 📄 ACE FILE GENE STRUCTURE (ace): Output gene structure in ACE file format.

    • ON
    • OFF - (Default)

  • 📊 GFF OUTPUT (gff): Output gene structure in GFF format.

    • ON
    • OFF - (Default)

  • 📝 EMBL FEATURE FOR DIANA (diana): Output EMBL feature table for DIANA.

    • ON
    • OFF - (Default)

  • 🌍 LOCAL/GLOBAL MODE (init): Choose between local or global alignment initialization.

    • Local - (Default)
    • Global

  • ✂️ SPLICE SITE (splice): Splice site model to use.

    • Modelled - (Default)
    • GT/AG only

  • 🎲 RANDOM (NULL) MODEL (random): Type of random model for scoring.

    • Synchronous model - (Default)
    • Flat model

  • ↔️ BOTH STRANDS (both): Search for genes on both DNA strands.

    • ON
    • OFF - (Default)

  • ⚙️ ALGORITHM (alg): Select the algorithm version.

    • GeneWise 623 - (Default)
    • GeneWise 2193

4️⃣ Submit Your Job

  • Once your sequences are 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 the predicted gene structure, including exon-intron boundaries, translation, and alignment of your query protein to the genomic DNA.
  • The output format will depend on the options selected (e.g., pretty ASCII, GFF, EMBL features).
  • ⭐ Tip: Review the alignment carefully, especially around splice sites, to confirm the accuracy of the gene prediction.

💬 Need Help?

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