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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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Biology, Academics

Category:- Biology
Reference No.:- M92298107

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