The answer, for bacteria and yeast genes are used to make protein. They start with a 3-base sequence that signals "start making protein," have some sequences that tell the cell which amino acids to put together to make the protein, and end with a 3-base sequence that signals "stop making protien." 3-base "stop" sequences occurs pretty frequently in the genome (just by random chance), so, if you find a long sequence that doesn't have a "stop" sequence, you can be pretty sure it's a gene. For more complicated organisms (like humans), it's much more difficult to tell what's a gene and what isn't, without figuring out what a gene does (because lots of human genes have what look like "stop" sequences in the middle of the gene)--but there are computer models of how genes appear different than "junk" DNA, that can be used to predict what is and isn't a gene. These aren't perfect, but they're fairly accurate.