Showing papers presented at "International Conference on Bioinformatics in 2001"

Selection of optimal DNA oligos for gene expression arrays

Abstract: Motivation: High density DNA oligo microarrays are widely used in biomedical research. Selection of optimal DNA oligos that are deposited on the microarrays is critical. Based on sequence information and hybridization free energy, we developed a new algorithm to select optimal short (20–25 bases) or long (50 or 70 bases) oligos from genes or open reading frames (ORFs) and predict their hybridization behavior. Having optimized probes for each gene is valuable for two reasons. By minimizing background hybridization they provide more accurate determinations of true expression levels. Having optimum probes minimizes the number of probes needed per gene, thereby decreasing the cost of each microarray, raising the number of genes on each chip and increasing its usage. Results: In this paper we describe algorithms to optimize the selection of specific probes for each gene in an entire genome. The criteria for truly optimum probes are easily stated but they are not computable at all levels currently. We have developed an heuristic approach that is efficiently computable at all levels and should provide a good approximation to the true optimum set. We have run the program on the complete genomes for several model organisms and deposited the results in a database that is available on-line (http://ural.wustl.edu/∼lif/probe.pl). Availability: The program is available upon request.

A.I. (Inteligencia Artificial)

Abstract: E n los últimos años nos hemos acostumbrado a ver soluciones de automatización y control en que la utilización de técnicas de inteligencia artificial aporta beneficios contrastables. Varias marcas comercializan reguladores borrosos o combinados (por ejemplo, PID con control anticipativo borroso), o incluyen mecanismos de ajuste fino de parámetros basados en lógica borrosa. Ocasionalmente, las redes neuronales se han utilizado en el modelado y control de sistemas no lineales. La implantación masiva de sistemas de adquisición y registro de datos (en ocasiones impuestos por requisitos de trazabilidad y calidad) ha permitido un mejor conocimiento de las plantas, que se ha reflejado en las tareas de ingeniería y gestión. Se persigue, por tanto, la reutilización de este conocimiento directamente en planta para detectar y diagnosticar en línea. El beneficio recaerá tanto en la mejora de planes de mantenimiento (ajuste de tiempos, predicción de fallos, asignación de recursos, planificación, etc.) como en la toma de decisiones por parte del supervisor (reducción del tiempo para conocer las causas) para evitar situaciones catastróficas.

Database-driven multi locus sequence typing (MLST) of bacterial pathogens

Abstract: Motivation: Multi Locus Sequence Typing (MLST) is a newly developed typing method for bacteria based on the sequence determination of internal fragments of seven house-keeping genes. It has proved useful in characterizingand monitoring disease-causing and antibiotic resistant lineages of bacteria. The strength of this approach is that unlike data obtained using most other typing methods, sequence data are unambiguous, can be held on a central database and be queried through a web server. Results: A database-driven software system (mlstdb) has been developed, which is used by public health laboratories and researchers globally to query their nucleotide sequence data against centrally held databases over the internet. The mlstdb system consists of a set of perl scripts for defining the database tables and generating the database management interface and dynamic web pages for querying the databases.

Clustering of translocation breakpoints

Abstract: Translocation, a physical movement of genetic material from one chromosome to another, can aberrantly juxtapose portions of two cellular genes. This type of fusion may disrupt cellular function by producing novel, biologically-active fused genes, or by the activation of normally quiescent growth-associated genes. Either of these mechanisms provides a putative oncogenic stimulus and, indeed, several gene fusions from translocations have been identified in leukemias, lymphomas, and sarcomas. While the biological activity of the oncogenic effects of genes involved in translocations are under intensive study, little is known regarding the formation of translocation fusions themselves. The locations of these fusions are typically independent of the resultant oncogenic protein as long as they take place within certain bounded regions within the genes. Because of this independence a patterned, in particular clustered, distribution of fusion breakpoints within a given region will potentially yield relevant information about the etiology of the fusion. The statistical analysis of translocation breakpoints has, accordingly, focused on the extent to which they cluster. Somewhat questionable methods have been employed in this regard. After highlighting these shortcomings, we introduce a variety of approaches including scan statistics, smoothed bootstrap, and gap statistics, that provide a comprehensive means for appraising clustering. We apply this battery to TEL-AML1 translocations, the most common translocation in childhood acute lymphoblastic leukemia. Results obtained indicate generally weaker evidence for clustering than previously reported, and also highlight differences between the statistical approaches.

Solid Edge versión 9

Abstract: Solid Edge de la compania UGS, es un potente entorno de CAD 3D de rango medio, especialmente indicado para el diseno de maquinaria y equipos industriales. La version 16 de Solid Edge reune todo un amplio conjunto de novedades y funcionalidades que como principal objetivo, intentan mejorar la produccion y seguimiento del diseno de productos complejos.