Today, we have very powerful and effective machines and methods to sequence and analyze DNA sequences. Almost every week, new genomes are added to sequence databases. However, those data are useless without additional annotations. Genes need to be found and their functions defined. Experimental work is too slow to analyze each sequence of a potential gene but computational methods facilitate such analyses. Here, we review the methodology, potential problems and constraints in genes finding and their annotation. We describe some new approaches including comparative genomics.