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.
Attachment:- Assignment Files.rar