A comparative analysis of existing oligonucleotides selection algorithms for microarray technology

In system biology, DNA microarray technology is an indispensable tool for the biological analysis involved at the level of the whole genome. Among the sophisticated analytical problems in microarray technology at the front and back ends, respectively, are the selection of optimal DNA oligonucleotides (henceforth oligos) and computational analysis of the genes expression data. A computational comparative analysis of the methods used to select oligos is important since the design and quality of the microarray probes are of critical importance for the hybridization experiments as well as subsequent analysis of the data. In an attempt to enhance efficient and effective design at the front end, a computational comparative analysis was performed on oligos selection tools using the barley ESTs, as well as the Saccharomyces cerevisiae, Encephalitozoon cuniculi and human genomes. The analysis also shows that a large number of the existing tools are difficult to install and configure. For cross hybridization test, most rely on BLAST and therefore design ill specific oligonucleotides. Furthermore, most are non-intuitive to use and lack important oligo design and software features

Systems Biology and the Development of Vaccines and Drugs for Malaria Treatments

The sequencing race has ended and the functional race has already begun. Microarray technology enables simultaneous gene expression analysis of thousands of genes, enabling a snapshot of an organisms’ transcriptome at an unprecedented resolution. The close correlation between gene transcription and function, allow the inference of biological processes from the assessed transcriptome profile. Among the sophisticated analytical problems in microarray technology at the front and back ends respectively, are the selection of optimal DNA oligos and computational analysis of the genes expression. In this review paper, we analyse important methods in use today in customized oligos design. In the course of executing this, we discovered that the oligos designer algorithm hanged on gene PFA0135w of chromosome 1, while designing oligos for the gene sequences of Plasmodium falciparum. We do not know the reason for this yet, as the algorithm runs on other sequences like the yeast (Saccharomyces cervisiae) and Neurospora crassa. We conclude the paper highlighting the procedures encompassing the back end phase and discuss their application to the development of vaccines and drugs for malaria treatment. Note that, malaria is the cause of significant global morbidity and mortality with 300-500 million cases annually. Our aims are not ends, but a means to achieve the following: Iterate the need for experimental biologists to (i) know how to design their customized oligos and (ii) have some idea about gene expression analysis and the need for cooperation between experimental biologists and their counterpart, the computational biologists. These will help experimental biologists to coordinate very well the front and the back ends of the system biology analysis of the whole genome effectively

An Improved Stock Price Prediction using Hybrid Market Indicators

In this paper the effect of hybrid market indicators is examined for an improved stock price prediction. The hybrid market indicators consist of technical, fundamental and expert opinion variables as input to artificial neural networks model. The empirical results obtained with published stock data of Dell and Nokia obtained from New York Stock Exchange shows that the proposed model can be effective to improve accuracy of stock price prediction

An Evaluation of Foreign Exchange Intervention and Monetary Aggregates in Nigeria (1986- 2003)

The paper investigates the impact of foreign exchange intervention in the Nigerian foreign exchange market using an Autoregressive Distributed Lag (ARDL) modeling approach. Quarterly time series data spanning 1986:1 to 2003:4 are used and a number of statistical tools are employed to verify this hypothesis. The study examines stochastic characteristics of each time series by testing their stationarity using Phillip Perron (PP) test. This is followed by performing cointegration test using Johansen technique. The existence of co-integration motivates us to estimate the error correction model for broad money, M2. The overall finding from all the techniques employed is that foreign exchange intervention in Nigeria is sterilized because the cumulative aid, which constitute part of foreign exchange inflows, and net foreign assets variables, which are proxies for intervention, are not significant. Thus, paper concludes by recommending, among others, that the use of stock of external reserves to support the exchange rate through increased funding of the foreign exchange market should be encouraged.Nigeria; Foreign Exchange Intervention; Co-integration and Auto-regressive Distributed Lag