Vortex

Vortex for Bioinformatics

Powerful, easy-to-use data visualization and analysis program that is widely adopted for scientific research.

Vortex for Bioinformatics extends Vortex with capabilities that allow all bioscientists to easily analyze and visualize their genomic, proteomic, antibody design, metabolomics and peptide data. Vortex for Bioinformatics makes it easy to load and view sequence and structure data. Standard bioinformatics analyses are integrated and simple to run directly form the graphical UI, and novel analyses such as biological structure/sequence activity relationship (BSAR) support scientific decision making to enhance the progress of discovery projects.

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What it does

Vortex for Bioinformatics enables scientists to load sequence and structure data from files or databases to create tables of live sequences and structures in Vortex. Sequence displays are interactive and the user can set a variety of display modes including linear and hyperbolic, and one- and three- letter codes.

Users can then apply standard bioinformatics analyses to their sequences, including alignment to a reference sequence, and cross alignment of a set of sequences to a reference set and clustering. A variety of methods are built in and, for less experienced users, the software will automatically select the most appropriate algorithm based on the data. So, for example, different methods will be appropriate for the alignment of very small sets of very short sequences, versus a cross comparison between very large sets of much longer sequences. As well as applying all the standard visualizations from Vortex, users can select visualizations appropriate to this kind of data such as CIRCOS plots and BSAR plots.

Sequences can be annotated with text, other sequences, small molecules (conjugates) and oligomers. Users can add annotations manually or apply library searches to identify regions within the sequences such as CDRs. Ontologies can be loaded and integrated with the sequence data to provide powerful analyses. When activity data is loaded alongside the biomolecular data, a novel BSAR analysis and visualization method can be applied that relates that activity to the structure and/or sequence.

Expert bioinformaticians can use the scripting capabilities of Vortex to define new methods or to integrate other third-party code, and then make these available to their Vortex user community.

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Benefits

  • Enables all bioscientists to analyze their own data. Users do not need to be an expert bioinformatician or proficient at scripting to be able to user Vortex for Bioinformatics
  • Suitable for a broad range of bioscience disciplines including genomics, proteomics, metabolomics and antibody, protein and peptide design
  • Handles all relevant data types including sequences, conjugates, oligomers, proteins and peptides as well as small molecules
  • Standard bioinformatics analyses are built in and fully integrated including sequence alignment (multiple methods), cross alignment, sequence clustering, Prosite searching, library search (e.g. CDR and ORF detection)
  • High performance visualization and analysis even on very large amounts of data – fast enough for interactive visualization and analysis of a whole genome on a standard business laptop
  • Leverages the highly successful Vortex program that has been widely adopted across the pharma and biotech industry for cheminformatics and statistical analysis and visualization for many years, and so seamlessly integrates the new bioinformatics methods with the existing cheminformatics, statistics and charting techniques
  • Fully integrated with the Dotmatics suite as an integral part of biologics discovery workflows when used in conjunction with Studies Notebook for Biology, BioRegisterInventoryStudiesCascadeBrowser and Gateway

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Key Features

  • Load data from FastA, FastQ, (HELM in development) or directly from databases via Dotmatics Browser
  • Native handling of scientific data types including sequences, conjugates, oligomers, proteins and peptides as well as small molecules
  • Display sequences in hyperbolic or linear one line, or multiline representations of one-letter or three-letter codes
  • Display 3D structures of proteins and antibodies in a variety of modes including ribbon, CPK and surface
  • Display oligomer representations
  • Annotate sequences with text, other sequences, small molecules or oligomers
  • Sequence alignment (multiple methods), cross alignment, sequence clustering, BLAST and Prosite searching, library search, and ORF detection
  • BSAR (Biological Sequence/Structure Activity Relationship) analysis
  • Visualizations – CIRCOS plots, BSAR plots, in addition to a wide variety of regular plots (e.g. bar, scatter, pie, heatmap, tree and many more)
  • Load and display OBO and OWL ontologies