Vortex

Vortex for Bioinformatics

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

Vortex for Bioinformatics extends Vortex with capabilities that allow scientists engaged in biologics drug discovery and other biology research to easily analyze and visualize their data, including antibody sequences, genomic, proteomic, metabolomic, and peptide data. Vortex for Bioinformatics intrinsically understands biological data types, simplifying the process of loading and viewing sequence and structure data. Standard bioinformatics analyses are integrated and simple to run directly from the graphical user interface, and novel analyses such as biological structure/sequence activity relationship (BSAR) and matched pair analyses enhance scientific decision making to accelerate 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, cross alignment amongst a set of sequences, and clustering. A variety of sequence alignment methods are included, and using built-in intelligence users can allow the software to 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.

Vortex for Bioinformatics supports rich sequence annotation, including 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 antibody complementarity determining regions (CDRs). Ontologies can be loaded and integrated with sequence data to provide comprehensive information for 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.

Vortex for Bioinformatics is designed to be used by a wide variety of biologists, ranging from those primarily focused on laboratory work, through to expert bioinformaticians who 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 in a single place. 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 antibody design, protein and peptide analysis, genomics, proteomics, and metabolomics
  • Natively 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, and 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, or millions of shorter sequences, 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 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
  • Annotate sequences with text, other sequences, small molecules or oligomers
  • Search and browse sequence annotations
  • Supports antibody CDR numbering schemes such as Kabat and Chothia
  • Sequence edit mode allows direct editing of sequences for mutations, insertions, and deletions
  • Display 3D structures of proteins and antibodies in a variety of modes including ribbon, CPK, and surface
  • Display oligomer representations
  • Sequence alignment (multiple methods), cross alignment, antibody CDR 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