Open Reading Frames * (Roofs) are regions with no stop codes. All genes reside in long open reading frames * Note that stop codes in other reading frames have no effect on the * Can be searched in the genome sequence. Valid only for prokaryote and gene. Lower eukaryote. Protein Sequencing vs..
DNA sequencing * We compare protein sequences, not DNA, because protein is more conserved in evolution than DNA * The organism’s survival depends on the protein being functional, which means having the proper amino acids sequence * Since the emetic code is degenerate, many different DNA sequences will give identical * The protein 3-dimensional structure is even more conserved, because proteins. It is more closely related to enzyme activity than the amino acid sequence is.
BLAST * standard sequence alignment tool (BLAST = Basic Local Alignment Search Tool) * BLAST is based on the concept that if you compare the same (that is, homologous) protein from many different species, you can see that some amino acids readily substitute for each other and others almost never do. * Results are arranged with he best ones on top * The most important score is the Expect value