Vortex

Vortex for Biologics Discovery

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

Vortex includes many capabilities that allow scientists engaged in biologics drug discovery and other biology research to easily analyze and visualize their data. Vortex intrinsically understands biological data types, including peptide and nucleotide sequences, antibody structure and features, and modified residues, simplifying the process of loading, viewing and analyzing sequence and structure data. Many standard bioinformatics analyses are integrated and simple to run directly from the graphical user interface, and advanced analyses such as Biological Sequence Activity Relationships (B-SAR) and Matched Pair Analysis (MPA) enhance scientific decision making to accelerate the progress of discovery projects.

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What it does

Vortex for biologics discovery enables scientists to load sequence, structure, computational and experimental 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 sequence views, and one- and three- letter residue 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 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 B-SAR plots.

Vortex for biologics discovery supports rich sequence annotation. Types of annotations includes text, regions, other sequences, small molecules (e.g., 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 biomolecular data, B-SAR analysis and visualization can be applied that relates that activity to the structure and/or sequence.

Vortex for biologics discovery is designed to be used by a wide variety of biologists, ranging from those primarily focused on laboratory work, to computational biologists, and 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 wider Vortex user community.

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Benefits

  • Enables 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 biologics discovery
  • 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
  • Seamlessly integrates 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, SAM/BAM (e.g., Illumina NGS data), and HELM files 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
  • Detection of hot spots, PAM sites (for CRISPR analysis), and nuclease / protease cut sites
  • 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
  • B-SAR (Biological Sequence Activity Relationship) analysis and Matched Pair Analysis (MPA)
  • Visualizations – CIRCOS plots, B-SAR 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