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Given the genomic sequences for an organism, one of the first steps in identifying the genes is to identify the open reading frames (ORFs).
Given the genomic sequences for an organism, one of the first steps in identifying the genes is to identify the open reading frames (ORFs). An open reading frame is a maximal length sequence of the DNA that starts with a start codon ATG and ends with a stop codon (TAA, TAG, or TGA). In prokaryotes, a gene may occur within ORFs. In eukaryotes, the story is complicated by the presence of introns that are spliced out of the mRNA before translation. In this assignment, you will write a Python program that finds all the ORFs in a genomic sequence. A genomic sequence has 6 reading frames, corresponding to the six possible ways of translating the sequence into three-letter codons. Frame 1 treats each group of three bases as a codon, starting from the first base. Frame 2 starts at the second base, and frame 3 starts at the third base. Frames 4, 5, and 6 are defined in a similar way but refer to the opposite strand, which is the reverse complement of the first strand. Specifications: Write a Python program called "orfs" to find all the open reading frames (ORFs) in the input sequence. INPUT: The program will take in as input a file, which will contain any number of DNA sequences in the FASTA format: -A line beginning with a ">" is the header line for the next sequence. - All lines after the header contain sequence data. - There can be any number of sequences per file. Sequences may be split over many lines. Sequence data may be upper or lower case. - Sequence data may contain white space, which should be ignored. Ask the user for the minimum ORF to search for. The default is 50, which means your program should print out all ORFs with at least 50 bases.
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