Genome-wide identification of specific oligonucleotides using artificial neural network and computational genomic analysis

<p>Abstract</p> <p>Background</p> <p>Genome-wide identification of specific oligonucleotides (oligos) is a computationally-intensive task and is a requirement for designing microarray probes, primers, and siRNAs. An artificial neural network (ANN) is a machine learning technique that can effectively process complex and high noise data. Here, ANNs are applied to process the unique subsequence distribution for prediction of specific oligos.</p> <p>Results</p> <p>We present a novel and efficient algorithm, named the integration of ANN and BLAST (IAB) algorithm, to identify specific oligos. We establish the unique marker database for human and rat gene index databases using the hash table algorithm. We then create the input vectors, via the unique marker database, to train and test the ANN. The trained ANN predicted the specific oligos with high efficiency, and these oligos were subsequently verified by BLAST. To improve the prediction performance, the ANN over-fitting issue was avoided by early stopping with the best observed error and a k-fold validation was also applied. The performance of the IAB algorithm was about 5.2, 7.1, and 6.7 times faster than the BLAST search without ANN for experimental results of 70-mer, 50-mer, and 25-mer specific oligos, respectively. In addition, the results of polymerase chain reactions showed that the primers predicted by the IAB algorithm could specifically amplify the corresponding genes. The IAB algorithm has been integrated into a previously published comprehensive web server to support microarray analysis and genome-wide iterative enrichment analysis, through which users can identify a group of desired genes and then discover the specific oligos of these genes.</p> <p>Conclusion</p> <p>The IAB algorithm has been developed to construct SpecificDB, a web server that provides a specific and valid oligo database of the probe, siRNA, and primer design for the human genome. We also demonstrate the ability of the IAB algorithm to predict specific oligos through polymerase chain reaction experiments. SpecificDB provides comprehensive information and a user-friendly interface.</p

Genome-wide identification of specific oligonucleotides using artificial neural network and computational genomic analysis

<p>Abstract</p> <p>Background</p> <p>Genome-wide identification of specific oligonucleotides (oligos) is a computationally-intensive task and is a requirement for designing microarray probes, primers, and siRNAs. An artificial neural network (ANN) is a machine learning technique that can effectively process complex and high noise data. Here, ANNs are applied to process the unique subsequence distribution for prediction of specific oligos.</p> <p>Results</p> <p>We present a novel and efficient algorithm, named the integration of ANN and BLAST (IAB) algorithm, to identify specific oligos. We establish the unique marker database for human and rat gene index databases using the hash table algorithm. We then create the input vectors, via the unique marker database, to train and test the ANN. The trained ANN predicted the specific oligos with high efficiency, and these oligos were subsequently verified by BLAST. To improve the prediction performance, the ANN over-fitting issue was avoided by early stopping with the best observed error and a k-fold validation was also applied. The performance of the IAB algorithm was about 5.2, 7.1, and 6.7 times faster than the BLAST search without ANN for experimental results of 70-mer, 50-mer, and 25-mer specific oligos, respectively. In addition, the results of polymerase chain reactions showed that the primers predicted by the IAB algorithm could specifically amplify the corresponding genes. The IAB algorithm has been integrated into a previously published comprehensive web server to support microarray analysis and genome-wide iterative enrichment analysis, through which users can identify a group of desired genes and then discover the specific oligos of these genes.</p> <p>Conclusion</p> <p>The IAB algorithm has been developed to construct SpecificDB, a web server that provides a specific and valid oligo database of the probe, siRNA, and primer design for the human genome. We also demonstrate the ability of the IAB algorithm to predict specific oligos through polymerase chain reaction experiments. SpecificDB provides comprehensive information and a user-friendly interface.</p

A mobile agent-based active network architecture for intelligent network control

The innovation and evolution of network technologies and services to enhance network functionality have traditionally encountered the problems of backward-compatibility and standardization. To resolve the related issues, active networks have been introduced to enable specific customization of network functionality without the lengthy standard-mediated committee processes. In this paper, we exploit the capability of mobile agent technology to construct an active network architecture. We argue that the mobile agent can be a building block for specific network customizations, and introduction of new network functionality. Both integrated and discrete operational models of network customizations can be supported in our prototype implementation. For the service development and deployment, an abstract service structure and a service loading mechanism are presented. Furthermore, we provide an agent management/control mechanism and devise a service management/control mechanism, which is either not available or incomplete in the other related work. The proposed architecture allows new service introduction, and as a result, achieves improved network functionality

Genome-wide identification of specific oligonucleotides using artificial neural network and computational genomic analysis-5

<p><b>Copyright information:</b></p><p>Taken from "Genome-wide identification of specific oligonucleotides using artificial neural network and computational genomic analysis"</p><p>http://www.biomedcentral.com/1471-2105/8/164</p><p>BMC Bioinformatics 2007;8():164-164.</p><p>Published online 22 May 2007</p><p>PMCID:PMC1892811.</p><p></p>e results of PCR amplification for 15 genes are shown. () Electrophoretic analysis of human PCR products. Fourteen genes with correct size of PCR products are shown. () The success rates of PCR amplification for and human are presented. The total success rate was 95

Genome-wide identification of specific oligonucleotides using artificial neural network and computational genomic analysis-3

<p><b>Copyright information:</b></p><p>Taken from "Genome-wide identification of specific oligonucleotides using artificial neural network and computational genomic analysis"</p><p>http://www.biomedcentral.com/1471-2105/8/164</p><p>BMC Bioinformatics 2007;8():164-164.</p><p>Published online 22 May 2007</p><p>PMCID:PMC1892811.</p><p></p>ance occurred in training set TSfor both the test and validation sets