I have one sequence that composed of sequences of three genes. I should determine the direction of each gene, but two of these genes are disrupted, and I can't determine the initial codon. Does anyone knows how I can determine the direction of genes?
I'd first try translating it and looking to see if there are big regions that jump out at you that do not have stop codons in them. I normally use this tool for quick and dirty translations, it gives you all 6 reading frames. Also, you could just try BLASTXing your sequence if it is short enough. BLASTX translates your DNA in all 6 reading frames and will search the protein database for matching proteins. Most anything will have a hit in there, and if you get a hit it will show you the DNA sequence and reading frame that got translated. If your sequence is too big, break it down into smaller chunks until BLASTX works. One of your chunks will have your gene in it, and it will get a protein hit. You'll also need to break it up if you have two genes in one chunk, but you only get results for one of them because its longer and gives better hits.