Gives access to many free software tools for sequence analysis. EMBOSS aims to serve the molecular biology community. It permits the creation and the release of software in an open source spirit. This tool is useful for sequence analysis into a seamless whole. It is free of charge and is available in open source.
Classifies local conformations of DNA molecules beyond their traditional sorting to A, B and Z DNA forms. DNATCO provides an interface to robust algorithms assigning conformation classes called ntC to dinucleotides extracted from DNA-containing structures uploaded in protein data bank (PDB) format. The assigned dinucleotide ntC classes are further grouped into DNA structural alphabet ntA, to the best of our knowledge the first DNA structural alphabet. The results are presented at two levels: in the form of user friendly visualization and analysis of the assignment, and in the form of a downloadable, more detailed table for further analysis offline. The website is free and open to all users without login requirement.
Permits interactive visualization of ground states of specific dsDNA sequences of interest. cgDNAweb suits for double stranded DNA by employing a sequence-dependent, coarse-grain, rigid-base model. This web-interface focuses on visualizing ground state shape in various ways and allows users to display the output results in either 3D view or 2D plots panes. It can predict a Gaussian probability density function (PDF) for the dsDNA configuration.
Enables users to display multistranded structures via layout algorithms. RiboSketch is a program available through an online interface or directly as a desktop version. It aims to permits manipulation of diverse structures through its interactive editing environment, accessible in both online and offline formats. Layouts can be generated automatically, manually (assisted by practical commands), by force simulation, or through any combination of methods.
Generates an auditory display from DNA sequence information. DNA Sonification allows to apply a sonification algorithm to the selected DNA sequence. Users can apply different sonification algorithms and change options of these to repeatedly process a DNA sequence to produce a simple or complex auditory display. The software additionally provides diverse test sequences to highlight the characteristics of each algorithm and resultant auditory display.
Allows users to compute melting profiles. DNAmelt is numerically stable for arbitrary sequence lengths, avoiding underflow problems related to the extensivity of the free energy. It permits users to work on correlations between different base pairs, loop opening probabilities, and higher order moments for base pair opening.
Visualizes protein structures DNA/RNA sequences into a virtual reality (VR) environment. BioVR proposes a platform usable through Oculus Rift intending to facilitate an interactive browsing of genomic variants. The application aims to assists users in highlighting sequence-structure relationship of important residues of a protein. It was tested on a representation of the Gria2 gene of Rattus norvegicus.
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