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Showing 11 open source projects for "show"
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UniversalMer
A CLI k-mer counting tool for multiple sizes of k at once.
UniversalMer is a k-mer counting tool for multiple size of k at once. It is available for DNA, RNA, and protein sequences. The program counts and summarizes the exact frequency of all k-mers from 1-mer to a user-defined maximum length (kmax). Analyzing the k-mer spectrum across multiple values of k can be done in seconds. This program is designed for bioinformatics researchers and scientists. -
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Ionwinze
Spot the differences between samples, groups and classes
...The effectiveness of a medicinal plant, poisons in a mushroom, resistance and susceptibility to pest and diseases are not necessarily because of the compounds that give large peaks. These traits are determined by the different levels of specific metabolites which may show up only as very small peaks. How would it be possible to spot an important metabolite or two, from 1000’s that occur in cells and tissues? If those truly relevant metabolites were missed during peak-picking then the following stats, however sophisticated they may be, would fail. And how many peaks are there in a single LCMS run? ... -
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DNA patterns & application
A software for generating DNA patterns
...References: [1] Gagniuc and Ionescu-Tirgoviste: Eukaryotic genomes may exhibit up to 10 generic classes of gene promoters. BMC Genomics 2012, 13:512. [2] Gagniuc and Ionescu-Tîrgoviste. Gene promoters show chromosome specificity and reveal chromosome territories in humans, BMC Genomics 2013, 14:278. Source code VB6 (Visual Basic 6.0) -
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came
Identification of chromatin accessibility from NOMe-seq
...Results: In this article, we present CAME, a seed-extension based approach that identifies chromatin accessibility from NOMe-seq. The efficiency and effectiveness of CAME were demonstrated through comparisons with other existing techniques on both simulated and real data, and the results show that our method not only can precisely identify chromatin accessibility but also outperforms other methods. -
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Glycosylation Microviewer
An application create, simulate and adjust N-linked glycosylation.
...The application allow to simulate the network in dynamic form with various ODE solvers(Euler, Runge-Kutta etc). Genetic Algorithm is used to adjust the kinetic parameters of Michaelis-Menten equations in glycosylation reaction network. A dynamic plot is supplied to show the value of mole amout and mole fraction of various glycoform. Thanks to Alexey Balakin and Alessandro Presta. Alexey Balakin supply mathgl(https://sourceforge.net/projects/mathgl) that make the implementation of dynamic plot in this application easily. Alessandro Presta supply fga(https://sourceforge.net/projects/fga) that provide a powerful use of GA. -
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A bioinformatics tool to PRe-process and show INformation of SEQuence data. The tool is written in Perl and can be helpful if you want to filter, reformat, or trim your sequence data. It also generates basic statistics for your sequences.
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Pontos
Pontos calculates distance matrices from DNA sequence alignments.
...Ambiguities (things like R, Y, N, W, etc. in a DNA sequence) can be treated like: - consider ambiguities as always different; - consider ambiguity as partially different (e.g. R would be 0.5 different from A or G); - ignore ambiguities in each pairwise comparison; - remove all columns, globally, that show any ambiguity. Pontos was written in Linux, but should run in any system where Java works. Pontos is licensed under the GPL version 3. -
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3D Genome Tuner draws circular genome map and enables viewing multi-genomes in 3D context. It also provides genome analysis and sequence alignment, making it a powerful tool in genome studies and demonstrations.
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--UPDATE-- New Version is now integrated in the official PyMOL plugin repository! --UPDATE-- The BNI (Beyond Normal Interaction)- Tools is a plug in for the PyMOL molecular visualization system which adds additional functionalities and presets to the PyMOL GUI and also adds useful extended commands.
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videonetwork
A simulator for self-organizing video replication and more
...It is robust, scalable and adaptive. The transport path of content is exploited to replicate content and limited storage space is handled by clean-up mechanisms. We implemented a simulator to show the algorithm's performance and to test its behavior under real circumstances. It is easily extendable to support several new scenarios or changes to the algorithm (see replication and client models).
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