CLAP: A web-server for automatic classification of proteins with special reference to multi-domain proteins

Background: The function of a protein can be deciphered with higher accuracy from its structure than from its amino acid sequence. Due to the huge gap in the available protein sequence and structural space, tools that can generate functionally homogeneous clusters using only the sequence information, hold great importance. For this, traditional alignment-based tools work well in most cases and clustering is performed on the basis of sequence similarity. But, in the case of multi-domain proteins, the alignment quality might be poor due to varied lengths of the proteins, domain shuffling or circular permutations. Multi-domain proteins are ubiquitous in nature, hence alignment-free tools, which overcome the shortcomings of alignment-based protein comparison methods, are required. Further, existing tools classify proteins using only domain-level information and hence miss out on the information encoded in the tethered regions or accessory domains. Our method, on the other hand, takes into account the full-length sequence of a protein, consolidating the complete sequence information to understand a given protein better. Results: Our web-server, CLAP (Classification of Proteins), is one such alignment-free software for automatic classification of protein sequences. It utilizes a pattern-matching algorithm that assigns local matching scores (LMS) to residues that are a part of the matched patterns between two sequences being compared. CLAP works on full-length sequences and does not require prior domain definitions. Pilot studies undertaken previously on protein kinases and immunoglobulins have shown that CLAP yields clusters, which have high functional and domain architectural similarity. Moreover, parsing at a statistically determined cut-off resulted in clusters that corroborated with the sub-family level classification of that particular domain family. Conclusions: CLAP is a useful protein-clustering tool, independent of domain assignment, domain order, sequence length and domain diversity. Our method can be used for any set of protein sequences, yielding functionally relevant clusters with high domain architectural homogeneity. The CLAP web server is freely available for academic use at http://nslab.mbu.iisc.ernet.in/clap/.

Haemophilus influenzae Genome Database (HIGDB): A single point web resource for Haemophilus influenzae

Background: Haemophilus influenzae (H. Influenzae) is the causative agent of pneumonia, bacteraemia and meningitis. The organism is responsible for large number of deaths in both developed and developing countries. Even-though the first bacterial genome to be sequenced was that of H. Influenzae, there is no exclusive database dedicated for H. Influenzae. This prompted us to develop the Haemophilus influenzae Genome Database (HIGDB). Methods: All data of HIGDB are stored and managed in MySQL database. The HIGDB is hosted on Solaris server and developed using PERL modules. Ajax and JavaScript are used for the interface development. Results: The HIGDB contains detailed information on 42,741 proteins, 18,077 genes including 10 whole genome sequences and also 284 three dimensional structures of proteins of H. influenzae. In addition, the database provides ``Motif search'' and ``GBrowse''. The HIGDB is freely accessible through the URL:http://bioserverl.physicslisc.ernetin/HIGDB/. Discussion: The HIGDB will be a single point access for bacteriological, clinical, genomic and proteomic information of H. influenzae. The database can also be used to identify DNA motifs within H. influenzae genomes and to compare gene or protein sequences of a particular strain with other strains of H. influenzae. (C) 2014 Elsevier Ltd. All rights reserved.

Online_DPI: a web server to calculate the diffraction precision index for a protein structure

An online computing server, Online_DPI (where DPI denotes the diffraction precision index), has been created to calculate the `Cruickshank DPI' value for a given three-dimensional protein or macromolecular structure. It also estimates the atomic coordinate error for all the atoms available in the structure. It is an easy-to-use web server that enables users to visualize the computed values dynamically on the client machine. Users can provide the Protein Data Bank (PDB) identification code or upload the three-dimensional atomic coordinates from the client machine. The computed DPI value for the structure and the atomic coordinate errors for all the atoms are included in the revised PDB file. Further, users can graphically view the atomic coordinate error along with `temperature factors' (i.e. atomic displacement parameters). In addition, the computing engine is interfaced with an up-to-date local copy of the Protein Data Bank. New entries are updated every week, and thus users can access all the structures available in the Protein Data Bank. The computing engine is freely accessible online at http://cluster.physics.iisc.ernet.in/dpi/.

Hydrogen Bonds Computing Server (HBCS): an online web server to compute hydrogen-bond interactions and their precision

Hydrogen bonds in biological macromolecules play significant structural and functional roles. They are the key contributors to most of the interactions without which no living system exists. In view of this, a web-based computing server, the Hydrogen Bonds Computing Server (HBCS), has been developed to compute hydrogen-bond interactions and their standard deviations for any given macromolecular structure. The computing server is connected to a locally maintained Protein Data Bank (PDB) archive. Thus, the user can calculate the above parameters for any deposited structure, and options have also been provided for the user to upload a structure in PDB format from the client machine. In addition, the server has been interfaced with the molecular viewers Jmol and JSmol to visualize the hydrogen-bond interactions. The proposed server is freely available and accessible via the World Wide Web at http://bioserver1.physics.iisc.ernet.in/hbcs/.

Plataforma legislativa para a biodiversidade

Trata de uma contribuição do Grupo de Trabalho criado no âmbito da Comissão de Meio Ambiente e Desenvolvimento Sustentável (CMADS) da Câmara dos Deputados com intuito de fornecer instrumento aos parlamentares e à sociedade em geral no sentido de alcançar os objetivos da Convenção sobre Diversidade Biológica. Pretende, ainda, nortear as discussões entre parlamentares e sociedade sobre as prioridades nacionais e buscar soluções criativas e inovadoras que tenham a biodiversidade e a sustentabilidade como pilares centrais das políticas públicas.

Diseño y ejecución de una coreografía gimnástica grupal con música

Duración (en horas): De 41 a 50 horas .Nivel educativo: Grado

Etiquetagem e folksonomia : uma análise sob a óptica dos processos de organização e recuperação da informação na web

Estuda etiquetagem e folksonomia sob a óptica dos processos de organização e recuperação da informação na web. Utiliza a metodologia de revisão bibliográfica, além de estudo de usuários, pesquisa exploratória e descritiva de sítios da web.

Moodle, la plataforma para la enseñanza y organización escolar

Sencilla y Potente. Ecológica y económica. “Moodle” se extiende exponencialmente por los centros de enseñanza de todo el mundo. Es muy útil como herramienta para la enseñanza. Permite la gestión de la asignatura, y son muchas sus utilidades, desde colgar los más diversos contenidos multimedia (apuntes, videos, imágenes,…,) hasta poder evaluar las diferentes tareas de nuestros alumnos o realizar exámenes online. Resulta esencial para crear “objetos de aprendizaje” o “unidades didácticas” y para fomentar el autoaprendizaje y el aprendizaje cooperativo. También es la herramienta ideal para gestionar la organización de las comunidades educativas y permitir la comunicación y el trabajo en red entre sus distintos integrantes y con otros centros. Resultando especialmente útil para la integración e implementación de los currículos, la comunicación con las familias y su uso en el ámbito extraescolar. Con este artículo se pretende explicar de una manera clara y sencilla en que consiste moodle y cuales son sus diferentes posibilidades de uso para los centros, los profesores y los alumnos, siempre desde el punto de vista de un usuario no iniciado en las nuevas tecnologías.

Web resources to disseminate methodology in heritage documentation

Impreso por la Diputación Foral de Álava, D.L. VI-430/99.

Los programas de fidelización como plataforma de venta directa: clasificación de los titulares según la redención de billetes aéreos

[ES] Cada vez son más numerosos los programas de fidelización que ofrecen al titular la posibilidad de comprar puntos o conseguir premios, viajes o billetes aéreos pagando una parte de los mismos con dinero. Dicha característica, unida a la propia estructura y dinámica de los programas de fidelización y a la actual coyuntura del sector turístico, ha permitido desarrollar plataformas de venta directa desde las que ofrecer servicios a los titulares.

A identificação de metadados de assunto para a legislação federal brasileira : o caso do Sistema Legin Web da Câmara dos Deputados

Aponta aspectos que devem ser considerados na identificação de metadados de assunto granulares para a legislação federal brasileira. O objeto de estudo foi o Sistema de Legislação Informatizada (Legin Web) disponível no Portal da Câmara dos Deputados. Os objetivos específicos foram: identificar tipos de assuntos amplamente utilizados na indexação da legislação federal brasileira e aspectos do contexto de busca de informação que interferissem na identificação dos metadados de assunto; analisar possibilidades de metadados de assunto para a legislação federal com base em padrões de metadados e modelos de organização da informação abordados na literatura; e, com isso, propor metadados de assunto para a legislação federal brasileira. A ideia é usar esses metadados para diminuir a imprecisão dos resultados das pesquisas na legislação federal, tornando o processo mais rápido e eficiente.