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196.
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This program performs an alignment of multiple nucleotide or amino acid sequences. It recognizes the format of input sequences and whether the sequences are nucleic acid (DNA/RNA) or amino acid (proteins). The output format may be selected from in various formats for multiple alignments such as Phylip or FASTA. Clustal[nbsp]W is very well accepted.
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Description
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(no translation yet)
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Located in
Package: clustalw
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197.
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The output of Clustal[nbsp]W can be edited manually but preferably with an alignment editor like SeaView or within its companion Clustal[nbsp]X. When building a model from your alignment, this can be applied for improved database searches. The Debian package hmmer creates such in form of an HMM.
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Description
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(no translation yet)
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Located in
Package: clustalw
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198.
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MPI-distributed global sequence alignment with ClustalW
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Summary
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alineamiento de secuencia global distribuido en MPI con ClustalW
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Translated by
Morgus
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Reviewed by
Paco Molinero
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Located in
Package: clustalw-mpi
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199.
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ClustalW is a popular tool for multiple sequence alignment. The alignment is achieved via three steps: pairwise alignment, guide-tree generation and progressive alignment. ClustalW-MPI is an MPI implementation of ClustalW. Based on version 1.82 of the original ClustalW, both the pairwise and progressive alignments are parallelized with MPI, a popular message passing programming standard. The pairwise alignments can be easily parallelized since the many alignments are time independent on each other. However the progressive alignments are essentially not parallelizable because of the time dependencies between each alignment.
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Description
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ClustalW es una herramienta popular para la alineación de secuencias múltiples. El alineamiento es logrado mediante tres pasos: alineamiento de pares, generación de arboles de guías y alineamiento progresivo. ClustalW-MPI es una implementación MPI de ClustalW. Basado en la versión 1.82 del ClustalW original, ambos alienamientos progresivo y de pares son paralelizados con MPI, un estándar popular de programación de paso de mensajes. Los alineamientos de pares pueden ser fácilmente paralelizados debido a que los múltiples alineamientos son independientes del tiempo el uno del otro. Sin embargo los alineamientos progresivos son esencialmente no paralelizables debido a las dependencias de tiempo entre cada alineamiento.
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Translated and reviewed by
Paco Molinero
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Located in
Package: clustalw-mpi
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200.
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Here the recursive parallelism paradigm is applied to the linear space profile-profile alignment algorithm. This approach is more time efficient on computers with distributed memory architecture. Traditional approach that relies on precomputing the profile-profile score matrix has also been implemented. Results shown the latter is indeed more appropriate for shared memory multiprocessor computer.
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Description
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Aqí se usa el paradigma de paralelismo recursivo para el algoritmo de alineamiento en el espacio lineal perfil a perfil. Este acercamiento es mejor eficiente en el consumo de tiempo de computadores con la arquitectura de memoria distribuida. La tradicional aproximación que se basa en la precomputación de la matriz de puntuación de perfil-perfil también fue implementada. Los resultados muestran que el último es, de hecho, más apropiado para los ordenadores multiprocesador con memoria compartida.
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Translated by
Samuel Iglesias
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Reviewed by
Paco Molinero
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Located in
Package: clustalw-mpi
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201.
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ClustalX is suggested for its support for local realignments, seaview is a versatile editor of alignments.
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Description
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ClustalX se recomienda por su soporte para realineamientos locales, seaview es un editor de alineamientos versátil.
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Translated by
Paco Molinero
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Reviewed by
Paco Molinero
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Located in
Package: clustalw-mpi
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202.
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The original ClustalW/ClustalX can be found at URL: http://www.clustal.org/download/pre-2/
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Description
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El ClustalW/ClustalX original se puede encontrar en: http://www.clustal.org/download/pre-2/
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Translated and reviewed by
Paco Molinero
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Located in
Package: clustalw-mpi
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203.
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Multiple alignment of nucleic acid and protein sequences (graphical interface)
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Summary
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Alineamiento múltiple de secuencias de ácidos nucleicos y proteínas (interfaz gráfica)
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Translated by
DiegoJ
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Reviewed by
Paco Molinero
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Located in
Package: clustalx
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204.
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This package offers a GUI interface for the Clustal multiple sequence alignment program. It provides an integrated environment for performing multiple sequence- and profile-alignments to analyse the results. The sequence alignment is displayed in a window on the screen. A versatile coloring scheme has been incorporated to highlight conserved features in the alignment. For professional presentations, one should use the texshade LaTeX package or boxshade.
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Description
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Este paquete ofrece una interfaz gráfica para el programa de alineación de secuencia múltiple Clustal. Proporciona un entorno integrado para realizar múltiples alineaciones de secuencia y de perfil y analizar los resultados. El alineamiento de secuencias se muestra en una ventana por pantalla. Posee un esquema de colores versátil para resaltar las características conservadas en la alineación. Para presentaciones profesionales, debe usarse el paquete LaTeX texshade o boxshade.
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Translated by
Michael Vogt
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Located in
Package: clustalx
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205.
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The pull-down menus at the top of the window allow you to select all the options required for traditional multiple sequence and profile alignment. You can cut-and-paste sequences to change the order of the alignment; you can select a subset of sequences to be aligned; you can select a sub-range of the alignment to be realigned and inserted back into the original alignment.
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Description
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Los menús desplegables en la parte superior de la ventana permiten seleccionar todas las opciones necesarias para la secuencia múltiple tradicional y el perfil de la alineación. Puede cortar y pegar secuencias para cambiar el orden de la alineación; también puede seleccionar un subconjunto de secuencias a ser alineado; puede seleccionar un sub-rango de la alineación para ser realineado e insertado de nuevo en la alineación original.
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Translated by
Michael Vogt
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Located in
Package: clustalx
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