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.
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 will 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.
Print your output in FASTA format, with one header line for each ORF, followed by the DNA in the ORF. The header should be the same as the header in the input file, followed by a bar "|" followed by FRAME = POS = LEN = , where is the frame number (1-6)
is the genomic position of the start of the ORF (left end is base 1) is the length of the ORF (in bases) If N = 4, 5 or 6, then P should be a negative number that indicates the position of the start of the ORF from the right end of the sequence. The DNA in the ORF should be printed out with a space between each codon, and no more than 15 codons per line.
We are a professional custom writing website. If you have searched a question and bumped into our website just know you are in the right place to get help in your coursework.
Yes. We have posted over our previous orders to display our experience. Since we have done this question before, we can also do it for you. To make sure we do it perfectly, please fill our Order Form. Filling the order form correctly will assist our team in referencing, specifications and future communication.
2. Fill in your paper’s requirements in the "PAPER INFORMATION" section and click “PRICE CALCULATION” at the bottom to calculate your order price.
3. Fill in your paper’s academic level, deadline and the required number of pages from the drop-down menus.
4. Click “FINAL STEP” to enter your registration details and get an account with us for record keeping and then, click on “PROCEED TO CHECKOUT” at the bottom of the page.
5. From there, the payment sections will show, follow the guided payment process and your order will be available for our writing team to work on it.