Gene2EST: a BLAST2 server for searching expressed sequence tag (EST) databases with eukaryotic gene-sized queries

Expressed sequence tags (ESTs) are randomly sequenced cDNA clones. Currently, nearly 3 million human and 2 million mouse ESTs provide valuable resources that enable researchers to investigate the products of gene expression. The EST databases have proven to be useful tools for detecting homologous genes, for exon mapping, revealing differential splicing, etc. With the increasing availability of large amounts of poorly characterised eukaryotic (notably human) genomic sequence, ESTs have now become a vital tool for gene identification, sometimes yielding the only unambiguous evidence for the existence of a gene expression product. However, BLAST-based Web servers available to the general user have not kept pace with these developments and do not provide appropriate tools for querying EST databases with large highly spliced genes, often spanning 50 000–100 000 bases or more. Here we describe Gene2EST (http://woody.embl-heidelberg.de/gene2est/), a server that brings together a set of tools enabling efficient retrieval of ESTs matching large DNA queries and their subsequent analysis. RepeatMasker is used to mask dispersed repetitive sequences (such as Alu elements) in the query, BLAST2 for searching EST databases and Artemis for graphical display of the findings. Gene2EST combines these components into a Web resource targeted at the researcher who wishes to study one or a few genes to a high level of detail.

The MetaFam Server: a comprehensive protein family resource

MetaFam is a comprehensive relational database of protein family information. This web-accessible resource integrates data from several primary sequence and secondary protein family databases. By pooling together the information from these disparate sources, MetaFam is able to provide the most complete protein family sets available. Users are able to explore the interrelationships among these primary and secondary databases using a powerful graphical visualization tool, MetaFamView. Additionally, users can identify corresponding sequence entries among the sequence databases, obtain a quick summary of corresponding families (and their sequence members) among the family databases, and even attempt to classify their own unassigned sequences. Hypertext links to the appropriate source databases are provided at every level of navigation. Global family database statistics and information are also provided. Public access to the data is available at http://metafam.ahc.umn.edu/.

SQL Server Management Studio Express Instalación

Instalación de SQL Server Management Studio Express en un MS Windows 7 Profesional.

SQL Server Management Studio Express 01

Primeros pasos en el uso de este programa cliente de acceso y administración de SQL Server. Este cliente, en su versión Express, es gratuito. El ejemplo del vídeo se conecta con un servidor remoto SQL Server 2008 R2.

SQL Server Management Studio Express 02

Segunda parte de los primeros pasos en el uso de este programa cliente de acceso y administración de SQL Server. Este cliente, en su versión Express, es gratuito. El ejemplo del vídeo se conecta con un servidor remoto SQL Server 2008 R2. Modificar tablas. Exportar definiciones del esquema. Resultados a cuadrícula o texto. Guardar resultados.

Transacciones en SQL Server

Una introducción a los objetivos y contenidos de la sesión 2 del curso de Bases de Datos dentro del Máster Universitario en Desarrollo de Aplicaciones y Servicios Web de la Universidad de Alicante. Se describe someramente qué se entiende por una transacción y se nombran los niveles de aislamiento en SQL Server. Todo enfocado a la realización de los ejercicios-demostraciones de esos niveles de aislamiento. Ingenuo y con fallos de encuadre e iluminación clamorosos, pero no tiene más ambiciones que la de dejar constancia de algunas de las cosas que se dijeron en clase.

Ejemplos de transacciones en SQL Server

Descripción de cómo facilitar la ejecución de los ejercicios de la sesión de transacciones del moodle de la asignatura. Se trata de reorganizar las ventanas y hacer espacio para tener dos consultas a la vista. En cada una de ellas se mantendrán una o varias transacciones que pretendemos ejecutar simultáneamente. De esta forma podremos ver qué transacciones esperan a las otras y pasar de una a otra consulta con facilidad.

Paginación en SQL Server

Una introducción a los objetivos y contenidos de la sesión 3 del curso de Bases de Datos dentro del Máster Universitario en Desarrollo de Aplicaciones y Servicios Web de la Universidad de Alicante. El trabajo que permite la calificación de esta primera parte del curso se basa, precisamente, en lo que se describe en este vídeo. La paginación de resultados es una técnica que pretende agilizar el manejo remoto de grandes cantidades de datos. El ejemplo clásico es la navegación por un catálogo de productos. Si es el servidor el que, por el procedimiento que sea, divide la lista completa en páginas y solo envía una de ellas al cliente, estamos ahorrando en tiempo y uso de red. En SQL Server, para esta tarea, es fácil encontrar opiniones que desaconsejan el uso de cursores puesto que se supone que el entorno objetivo es de alta concurrencia. No obstante, se puede usar TOP() y ROW_NUMBER(). La sesión consiste en una serie de ejemplos sobre todas estas herramientas.

Tuning compilations by multi-objective optimization: Application to Apache web server

Modern compilers present a great and ever increasing number of options which can modify the features and behavior of a compiled program. Many of these options are often wasted due to the required comprehensive knowledge about both the underlying architecture and the internal processes of the compiler. In this context, it is usual, not having a single design goal but a more complex set of objectives. In addition, the dependencies between different goals are difficult to be a priori inferred. This paper proposes a strategy for tuning the compilation of any given application. This is accomplished by using an automatic variation of the compilation options by means of multi-objective optimization and evolutionary computation commanded by the NSGA-II algorithm. This allows finding compilation options that simultaneously optimize different objectives. The advantages of our proposal are illustrated by means of a case study based on the well-known Apache web server. Our strategy has demonstrated an ability to find improvements up to 7.5% and up to 27% in context switches and L2 cache misses, respectively, and also discovers the most important bottlenecks involved in the application performance.

Development and field test of a responsible alcohol service program. Volume II: server education program materials. Final report.

National Highway Traffic Safety Administration, Washington, D.C.

Wurst: a protein threading server with a structural scoring function, sequence profiles and optimized substitution matrices

Wurst is a protein threading program with an emphasis on high quality sequence to structure alignments (http://www.zbh.uni-hamburg.de/wurst). Submitted sequences are aligned to each of about 3000 templates with a conventional dynamic programming algorithm, but using a score function with sophisticated structure and sequence terms. The structure terms are a log-odds probability of sequence to structure fragment compatibility, obtained from a Bayesian classification procedure. A simplex optimization was used to optimize the sequence-based terms for the goal of alignment and model quality and to balance the sequence and structural contributions against each other. Both sequence and structural terms operate with sequence profiles.

SVRMHC prediction server for MHC-binding peptides

The binding between antigenic peptides (epitopes) and the MHC molecule is a key step in the cellular immune response. Accurate in silico prediction of epitope-MHC binding affinity can greatly expedite epitope screening by reducing costs and experimental effort. Recently, we demonstrated the appealing performance of SVRMHC, an SVR-based quantitative modeling method for peptide-MHC interactions, when applied to three mouse class I MHC molecules. Subsequently, we have greatly extended the construction of SVRMHC models and have established such models for more than 40 class I and class II MHC molecules. Here we present the SVRMHC web server for predicting peptide-MHC binding affinities using these models. Benchmarked percentile scores are provided for all predictions. The larger number of SVRMHC models available allowed for an updated evaluation of the performance of the SVRMHC method compared to other well- known linear modeling methods. SVRMHC is an accurate and easy-to-use prediction server for epitope-MHC binding with significant coverage of MHC molecules. We believe it will prove to be a valuable resource for T cell epitope researchers.