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A set of libraries aimed at creating powerful tree- and track-based visualisations for the web. Its modularity and rich API facilitate the development of many different visualisations ranging from simple species trees to complex visualisations comprising per-node data annotations or even simple genome browsers. The TnT libraries have been written in Javascript using the D3 library as its main dependency. It uses SVG to render all the visual elements in the browser.
I-PV / Interactive Protein Sequence Visualization
Allows to visualize user supplied protein sequence, conservation and single nucleotide variant (SNV) in a live presentable format. I-PV is an interactive data visualization software that comes with tools to extract sequence, conservation, specific features and SNVs between user defined regions in a formatted text layout with user defined number of items per line. An add-on included in the software allows to visualize point mutations in user supplied variation/vcf files.
A browser-based interactive exploration tool to investigate the functional and evolutionary features of protein sequences. The browser-based interface of ProViz provides numerous advantages, especially relating to ease of accessibility. Feature information is retrieved in an automated manner from resources describing protein modular architecture, post-translational modification, structure, sequence variation and experimental characterization of functional regions. These features are mapped to evolutionary information from precomputed multiple sequence alignments. Data are displayed in an interactive and information-rich yet intuitive visualization, accessible through a simple protein search interface. ProViz is a versatile tool that can aid biologist in many ways, for example, building hypotheses, designing experiments or understanding experimental results. The flexible customization options of ProViz also permit bioinformaticians to extensively customize the visualization, for example, by mapping data from high-throughput proteomic studies or adding the results of per residue predictive bioinformatic tools to the presented data.
A comprehensive R package for generating various numerical representation schemes of proteins and peptides from amino acid sequence. The package calculates eight descriptor groups composed of twenty two types of commonly used descriptors that include about 22,700 descriptor values. It allows users to select amino acid properties from the AAindex database, and use self-defined properties to construct customized descriptors. ProtrWeb is a user-friendly web server for calculating descriptors presented in the protr package.
IBS / Illustrator of Biological Sequences
A Java software for assisting experimentalists in drawing publication-quality diagrams of both protein and nucleotide sequences. With a dual-mode user interface, users are allowed to produce their own schematic diagrams for either protein or nucleotide sequences in a convenient manner. To provide a user-friendly software package, abundant graphical elements, such as polygons, brackets, curves and polylines, are available for representing functional elements or regulatory molecules. We anticipate this powerful tool will prove to be a great help to scientists for the purpose of visualizing biological sequences.
An integrated tool aimed at exploring the sequence, structural and functional diversity in protein families useful in homology modeling and in analyzing protein families in general. MODexplorer can be used to analyze sequence and structural conservation among the structures of similar proteins, to find structures of homologs solved in different conformational state or with different ligands and to transfer functional annotations. Furthermore, if the structure of the query is not known, MODexplorer can be used to select the modeling templates taking all this information into account and to build a comparative model.
Permits to visualize graphical representation of protein sequence features in the UniProt Knowledgebase, experimental proteomics and variation public datasets. ProtVista lays out, maps, orients, and renders position-based annotations for sequences. It allows users to add custom data services using the features JSON format. The tool offers an intuitive and compact representation of protein features, making it easier to highlight different data relationships that might otherwise be unclear or difficult to grasp.
A JavaScript library for creating interactive visualizations of biological sequences and various associated data. Protael allows users to generate high-quality vector graphics (SVG) and integrate it into web pages. Protael is capable of displaying multiple data types, such as sequence annotations, substitutions, posttranslational modifications, cleavage sites, disulfide bridges, various types of quantitative data, and alignments with known structures. Sequence features, annotations, quantitative data and aligned sequences can occupy multiple data tracks.
A BioJS component that lays out, maps, orients, and renders position-based annotations for protein sequences. This component is highly flexible and customizable, allowing the presentation of annotations by rows, all centered, or distributed in non-overlapping tracks. It uses either lines or shapes for sites and rectangles for regions. The result is a powerful visualization tool that can be easily integrated into web applications as well as documents as it provides an export-to-image functionality.
Computes sequences with features in pretty format. showseq displays one or more nucleic acid sequences, with features, in a style suitable for publication. Optionally, the sequence feature table can be displayed. The sequence can be translated, using the specified genetic code tables. Also recognition sites and/or cut sites of restriction enzymes from the REBASE database may be displayed. There are various other options for controlling how the sequence is displayed and numbered and the output can be formatted for HTML.
Visualizes significant conserved amino acid sequence pattern in groups based on probability theory. Compare to iceLogo, dagLogo can also visualize significant sequence patterns by clustering the peptides. In addition, there are several differences between dagLogo from iceLogo: (i) the sequence patterns can be grouped by charge, chemistry, hydrophobicity and etc., (ii) dagLogo accepts different length of aligned amino acid sequences and (iii) except Random, regional (called restricted in dagLogo) and terminal (called anchored) background model, the background sequence could be set to other regions of the genes in inputs and complementary set of the proteome.
Provides a graphical interface for basic comparative (homology) modeling using SCWRL and other programs. MolIDE takes an input target sequence and uses PSI-BLAST to identify and align templates for comparative modeling of the target. The sequence alignment to any template can be manually modified within a graphical window of the target-template alignment and visualization of the alignment on the template structure. MolIDE builds the model of the target structure on the basis of the template backbone, predicted side-chain conformations with SCWRL and a loop-modeling program for insertion-deletion regions with user-selected sequence segments.
RbDe / Residue-based Diagram editor
A web-based software that greatly simplifies the construction of schematic diagrams of proteins. Residue-based diagrams display the sequence of a given protein in the context of its secondary and tertiary structure. Such diagrams are frequently used to summarize mutations or sequence features, in the context of the overall topology of a protein. Users can import custom-diagram layouts, use them to render members of any protein family and generate high-quality output for publication purposes.
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