Basically I have a DNA sequence file somewhere on my computer. I need to select an ORF by using the START and STOP codons. That is, I need to find the sequences that lie between ATG and either of TTA, TAG, TGA. The sequence file is pretty long. What should be the exact program? Please help with a complete program. I tried the ones available on the internet, but they didn't work out
Also, another question. Some examples in the book show variables declared as my$DNA while some are $DNA. What is the difference?
Thanks in advance for your help