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Barracuda is a high-speed sequence aligner based on Sanger's BWA and utilizes the latest Nvidia CUDA architecture for accelerating alignments of sequence reads generated by next-generation sequencers.
...MGEScan-non-LTR is a software for the identification of non-LTR retrotransposons in genomic sequences, following a computational approach inspired by a generalized hidden Markov model (GHMM).
References:
1. M. Rho et al., "De novo identification of LTR retrotransposons in eukaryotic genomes", BMC Genomics (2007) 8:90.
2. M. Rho and H. Tang, "MGEScan-non-LTR: computational identification and classification of autonomous non-LTR retrotransposons in eukaryotic genomes", Nucleic Acids Research (2009) 37:21.
mean first passage times and node occupancies calculations
...Two methods are made available for which their efficiency is strongly dependent on the topology of the defined network: the combinatorial Hill technique and the Monte Carlo simulation method.
References:
M. Torchala, P. Chelminiak, M. Kurzynski and P. A. Bates, 'RaTrav: a tool for calculating mean first-passage times on biochemical networks', BMC Syst. Biol. 7, 130 (2013).
M. Torchala, P. Chelminiak and P. A. Bates, 'Mean first-passage time calculations: comparison of the deterministic Hill's algorithm with Monte Carlo simulations', Eur. Phys. J. B 85, 116 (2012).
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Corra [BMC Bioinformatics 2008] is a computational framework & tools for discovery proteomics using label free LC-MS and ATAQS [BMC Bioinformatics 2011] is a computational framework & tools for validation proteomics using SRM LC-MS method.
CoCOOT is an extended collaboration system of COOT(Crystallographic Object Oriendted Toolit). It operates an add-on of original Coot. It enables to collaboration through internet.