8.8 years ago by
I'm not sure if I'm understanding all of it well, but I have a few hints that I guess you could use:
For the finding restriction sites you can use the EMBOSS package, which is available to use either through web interfaces or command line, what ever you prefer. You can access it for direct web use in:
Basically you submit a sequence and it will try to find restriction sites for you. You can specify I think which enzymes to use. It will look for the restriction sites in both directions (I'm almost sure, I used this last time several years ago), so you don't need to worry about that yourself.
Regarding finding your genes, I'm guessing for what you write that you haven't actually defined the positions of them yet in your sequence. For this you classically need a gene marker (such as Glimmer3, Critica, there are probably some newer ones, haven't been in genome annotation field for a little while now) program/algorithm. You would normally use Glimmer in the command line, as there are many ways of training it, and it really depends on the data you have. Assuming that you are not familiarized with running unix programs, in the case of Glimmer, you can use an already trained bacterial version on:
Glimmer will tell you where you probably have genes in your sequence (where they end and where they start). The business is slightly more tricky than just finding start and stop codons ;-).
These two tools of course only make sense for microbial genomes. Good luck ;-).