copy; Wiley Publishing. 2007. All Rights Reserved..ppt

? Wiley Publishing. 2007. All Rights Reserved. Learning Objectives Discover how to manipulate your DNA sequence on a computer, analyze its composition, predict its restriction map, and amplify it with PCR Find out about gene-prediction methods, their potential, and their limitations Understand how genomes and sequences and assembled Outline Cleaning your DNA of contaminants Digesting your DNA in the computer Finding protein-coding genes in your DNA sequence Assembling a genome Cleaning DNA Sequences In order to sequence genomes, DNA sequences are often cloned in a vector (plasmid, YAC, or cosmide) Sequences of the vector can be mixed with your DNA sequence Before working with your DNA sequence, you should always clean it with VecScreen Computing a Restriction Map It is possible to cut DNA sequences using restriction enzymes Each type of restriction enzyme recognizes and cuts a different sequence: EcoR1: GAATTC BamH1: GGATCC There are more than 900 different restriction enzymes, each with a different specificity The restriction map is the list of all potential cleavage sites in a DNA molecule You can compile a restriction map with /cutter Making PCR with a Computer Polymerase Chain Reaction (PCR) is a method for amplifying DNA PCR is used for many applications, including Gene cloning Forensic analysis Paternity tests PCR amplifies the DNA between two anchors These anchors are called the PCR primer Designing PCR Primers PCR primes are typically 20 nucleotides long The primers must hybridize well with the DNA On , find the best location for the primers: Most stable Longest extension Analyzing DNA Composition DNA composition varies a lot Stability of a DNA sequence depends on its G+C content (total guanine and cytosine) High G+C makes very stable DNA molecules Online resources are available to measure the GC content of your DNA sequence Predicting Genes The most important analysis carried out on DNA sequences is gene prediction Gene prediction requires diff