Write a simple prokaryotic gene prediction program

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Write a simple prokaryotic gene prediction program based on the promoter, Shine-Delgarno sequences.

Prokaryotic Gene Prediction Algorithm

Gene sequences including an ORF of a certain length, a Shine-Dalgarno sequence, and promoter, are candidate genes

1. Search for the next start codon. If no start codon is found, end.

2. Search for a stop codon in the same reading frame as the start codon. Continue only if the ORF length is greater than a threshold (e.g., 100 amino acids). Otherwise start over.

3. Search for a Shine-Dalgarno sequence 3-7 bases upstream of the start codon. The sequence should pass a matching threshold (e.g., 5/6 identity). If not found, start over.

4. Search 500 nucleotides upstream of the Shine-Dalgarno sequence for a promoter. The TTGACA promoter should be located 15-19 nucleotides upstream of TATAAT. Allow for one mismatch in each sequence.

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Reference no: EM131489372

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len1489372

5/9/2017 2:48:04 AM

Write a simple prokaryotic gene prediction program (pg 12 of the Gene Prediction notes), based on the promoter, Shine-Delgarno sequences, and open reading frames coding for at least 100 amino acids. Note: you may use Biopython for this assignment. Gene sequences including an ORF of a certain length, a Shine- Dalgarno sequence, and promoter, are candidate genes. Search for the next start codon. If no start codon is found, end. Gene Prediction in Eukaryotes must preserve the correct reading frame and involves prediction of the promoter.

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