Bioinformatics Resources (bioinformatics + resource)

Distribution by Scientific Domains

Selected Abstracts

Mutation-specific database and bioinformatics resource for DMD

HUMAN MUTATION, Issue 6 2009
Kevin M. Flanigan
No abstract is available for this article. [source]

Molecular biology of aromatic plants and spices.

A review.
Abstract In recent years, molecular tools have been used to help to elucidate some aspects of genetic diversity in aromatic species, the genetic relationships between different cultivars and comparisons of molecular marker analysis to the chemical composition of plants. In this review, an explanation of the most important techniques involving molecular markers is given. A literature survey on molecular markers is presented, with some examples from aromatic plants and spices. However, understanding what controls flavour and aroma production in plants is not an easy task to accomplish. Several aspects of plant secondary metabolism, in particular volatiles production in aromatic plants, are still unknown. The route from genomics to proteomics is not well documented, although some research with model plants has already been performed. To address the question of the synthesis of volatiles, two different approaches are possible and summarized in this review: first, the biochemical and genetic approach; and second, approaches involving functional genomics. Finally, a brief survey of bioinformatics resources is presented. Copyright 2010 John Wiley & Sons, Ltd. [source]

Current Applications of Microarrays in Head and Neck Cancer Research

FRCS Eng, Giles C. Warner MSc
Abstract Objectives/Hypothesis: The objective was to introduce microarray technology and its applications in cancer research to the head and neck clinician. Study Design: Literature review combined with methodology and examples from the authors' experiences with microarray analysis of tumors of the head and neck. Methods: Search of literature and the authors' experience was made for technical details, alternative methods of data analysis, available bioinformatics tools, and applications of microarrays in cancer research. Results: Microarrays allow the simultaneous analysis of the expression of thousands of genes. The use of a well-developed microarray study design leads to informative results. There are various bioinformatics resources widely available to aid in the analysis of microarray data. However, there is not yet a gold standard for analysis because this methodology is still evolving. Conclusion: Microarray studies may allow researchers to identify genetic changes relevant to diagnosis and prognosis in patients with head and neck cancer. Although still relatively new, this powerful methodology has immense potential to aid in understanding of the genetic changes that are important in head and neck cancer. [source]

SNP Discovery and Haplotype Analysis in the Segmentally Duplicated DRD5 Coding Region

Donna J. E. Housley
Summary The dopamine receptor 5 gene (DRD5) holds much promise as a candidate locus for contributing to neuropsychiatric disorders and other diseases influenced by the dopaminergic system, as well as having potential to affect normal behavioral variation. However, detailed analyses of this gene have been complicated by its location within a segmentally duplicated chromosomal region. Microsatellites and SNPs upstream from the coding region have been used for association studies, but we find, using bioinformatics resources, that these markers all lie within a previously unrecognized second segmental duplication (SD). In order to accurately analyze the DRD5 locus for polymorphisms in the absence of contaminating pseudogene sequences, we developed a fast and reliable method for sequence analysis and genotyping within the DRD5 coding region. We employed restriction enzyme digestion of genomic DNA to eliminate the pseudogenes prior to PCR amplification of the functional gene. This approach allowed us to determine the DRD5 haplotype structure using 31 trios and to reveal additional rare variants in 171 unrelated individuals. We clarify the inconsistencies and errors of the recorded SNPs in dbSNP and HapMap and illustrate the importance of using caution when choosing SNPs in regions of suspected duplications. The simple and relatively inexpensive method presented herein allows for convenient analysis of sequence variation in DRD5 and can be easily adapted to other duplicated genomic regions in order to obtain good quality sequence data. [source]