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    BMCBI
    2005
    162views more  BMCBI 2005»
    Accelerated probabilistic inference of RNA structure evolution
    14 years 9 months ago
    Accelerated probabilistic inference of RNA structure evolution
    Download  biowiki.org
    Background: Pairwise stochastic context-free grammars (Pair SCFGs) are powerful tools for evolutionary analysis of RNA, including simultaneous RNA sequence alignment and secondary...
    Ian Holmes
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    BMCBI
    2005
    169views more  BMCBI 2005»
    MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes
    14 years 9 months ago
    MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes
    Download  www.biomedcentral.com
    Background: Cis-regulatory modules are combinations of regulatory elements occurring in close proximity to each other that control the spatial and temporal expression of genes. Th...
    Voichita D. Marinescu, Isaac S. Kohane, Alberto Ri...
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    SASP
    2009
    IEEE
    291views Hardware» more  SASP 2009»
    A parameterisable and scalable Smith-Waterman algorithm implementation on CUDA-compatible GPUs
    15 years 4 months ago
    A parameterisable and scalable Smith-Waterman algorithm implementation on CUDA-compatible GPUs
    Download  www.see.ed.ac.uk
    —This paper describes a multi-threaded parallel design and implementation of the Smith-Waterman (SM) algorithm on compute unified device architecture (CUDA)-compatible graphic pr...
    Cheng Ling, Khaled Benkrid, Tsuyoshi Hamada
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    BMCBI
    2005
    100views more  BMCBI 2005»
    Scoredist: A simple and robust protein sequence distance estimator
    14 years 9 months ago
    Scoredist: A simple and robust protein sequence distance estimator
    Download  sonnhammer.sbc.su.se
    Background: Distance-based methods are popular for reconstructing evolutionary trees thanks to their speed and generality. A number of methods exist for estimating distances from ...
    Erik L. L. Sonnhammer, Volker Hollich
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    NAR
    2008
    101views more  NAR 2008»
    PVS: a web server for protein sequence variability analysis tuned to facilitate conserved epitope discovery
    14 years 9 months ago
    PVS: a web server for protein sequence variability analysis tuned to facilitate conserved epitope discovery
    Download  imed.med.ucm.es
    We have developed PVS (Protein Variability Server), a web-based tool that uses several variability metrics to compute the absolute site variability in multiple protein-sequence al...
    Maria Garcia-Boronat, Carmen M. Diez-Rivero, Ellis...
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