In this exercise we will run a genomic DNA sequence against some gene prediction programs, and we will analyze the differences between predictions and annotations of the real gene.

1. Tools

• geneid (gene prediction program)
• Genscan (gene prediction program)
• MetaGene (gate to several gene prediction program)

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2. Get seq. and annotation

• Get the DNA sequence: HS307871
• Get the annotations (EMBL input)

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3. Run geneid

• Connect to the geneid server
• Paste DNA sequence
• Run geneid with different parameters:
  1. Searching signals: Select acceptors, donors, start and stop codons. Look for them in the real annotation of the sequence

  2. Searching exons: Select All exons and try to find the real ones

  3. Finding genes: You do not need to select any option (default behaviour). Compare the predicted gene with the real gene

• ANALIZE THE RESULTS

  Predicted sites Predicted exons Predicted genes

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4. Run Genscan

• Connect to the Genscan server
• Paste DNA sequence
• Run Genscan

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6. Compare Predictions

Compare geneid and Genscan predictions checking this plot

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7. Run Metagene

• Connect to the MetaGene server
• Fill in sequence name and e-mail address (not compulsory)
• Paste DNA sequence
• Run MetaGene
• Wait for a couple of minutes, monitoring the search process
• Check Current Search Results
• Annotate Results
• Tools: Statistics summary
• Tools: Analysis