Rice Chromosome 4 BAC Screening, Sequencing And Annotation; Dampable Waves On Nucleic Acids And The Programming Of A Primer Designing Tool Suite

We newly adopted Pool PCR (PCR with multiplex primer pairs and templates) method to search for clones that are specifically on rice chromosome 4. Comparing to the traditional hybridization method, Pool PCR has much higher efficiency, sensitivity, specificity and reusability. The novelty of our work also resides in our appropriately grouping the primers and a deliberately designed PCR condition. PMT software suite, which we developed later, further enhanced such novelty. Then we devoted ourselves to the large-scale sequencing of rice chromosome 4. After that, we fully made use of various bioinformatic tools and sequence resources on the Internet for the detailed annotation of rice chromosome 4. The interaction between nucleotides on nucleic acid sequences is the basis for any bioinformatic model for nucleic acids, so we have designed a new algorithm to study the average interaction intensity between any two nucleotides on nucleic acid sequences. Using rice chromosome 4 sequence, E. coli whole genome sequence, 27838 Arabidopsis thaliana coding sequences, and 28469 Oryza sativa ssp. japonica full-length cDNAs as the materials, we found that the interactions between any two nucleotides on nucleic acid sequences are clearly and closely related with two dampable wavelike patterns along the sequences. We named the two kinds of waves "Bat wave" and "Whale wave" according to their different wavelengths. Bat wave has a large amount of damping and may mediate the interactions between nucleotides within a gene, while Whale waves may act as an intergenic messenger across far distances for their small amout of damping. A gene is much shorter than a chromosome maybe because Bat wave have much more damping than Whale wave. Calculation results suggested that most organisms select ATG as the start codon probably for the sake of Bat wave consistency. Further studies on Bat-Whale wave may provide new clues for gene prediction and genome structure study. In order to improve the performance of PCR, especially multiplex PCR, we have developed a software suite: PMT. PMT includes three applications. We have integrated almost all the now-existing primer designing criteria into PMT suite, and have used the latest Nearest-neighbor model. Through a series of actual PCR experiments, we proved that PMT is able to design high-quality primers and promote the performance of multiplex PCR. Comparing to other designing software, PMT has considerable novelty and superiority for its robustness, friendliness and high efficiency; its comprehensive consideration of primer designing criteria, its multiplex PCR primer set evaluation functionality and an experiment-based formula to calculate the optimum annealing temperature.