This project is read-only.

CAT UI Dictionary Terms


  • Alignment: A Sequence that contains a pattern of sequence elements, gaps and annotation characters.
  • Alignment Container: A generic container of Alignments(s) which behaves as a 2D grid of Row(s) and Column(s). The null case or empty set is 0 Rows and 0 Columns. Each Row of the grid can contain one Alignment, and the same Alignment can appear in multiple Rows. Any position can be accessed by Column and Row. Alignment Containers may contain Structural Relationships or Taxonometric Relationships.
  • Alignment Curator: Privileged User able to visualize and edit full alignments stored in the rCAD Database.
  • Annotation: Any character that can be inserted into an Alignment that is not a gap character or a sequence character.
    • We have a somewhat "hierarchical" categorization of annotation characters that would fall in the "annotation" family
      • Structure-based
        • (, ) Enclose hairpin loops
        • | Used to indicate helix discontinuities, on pipe indicator is opposite (on the helix 5' or 3') the discontinuity. This is placed w/respect to the reference sequence/structure.
      • "either-or"/context-based
        • {[,]} Identifies start and end of well-behaved variable regions, in the rRNA alignments using the previous e Coli nucleotide to refer to region.
        • <, > Similar to {[,]}, but for a less well-behaved region.
      • = or * Sometimes used to represent gap characters to get around a limitation of AE2 where you can't slide a group that contains a gap.
      • Plus sign (+) indicates insertions
      • // Indicates a fragmented gene. Represent that two sequences that look continuous on the alignment are not really continuous in the genome (excludes the intron case, where '+ ' is used instead)
  • Any User: Container term which is used to mark an operation as applicable to all possible User(s).
  • Artifact: Logical elements (Biological) that are represented as objects in a software program.


  • ''Biological Analyst:'' A User that is not able to make modifications to the rCAD Database.


  • Clean: The Artifact is in an unchanged state from when it was loaded into the system.
  • Column: The Artifact that represents one dimension of the Alignment grid. Each Row has only one element in a given Column.
  • Context: A collection of properties and filters which can be used in an expression to define a data collection which will be visualized in one or more View(s)''.


  • Developer: A User that has no restrictions within the system as far as what data they can visualized and edit in the rCAD Database. Basically a super-user.
  • Dirty: The Artifact is in a changed state from when it was loaded into the system.


  • Gap: Meta-character which is placed in Column(s) in an Alignment where a given Sequence does not have a Nucleotide to place in that Column.
  • Group: User-based, emperically-defined selection of Row(s) in an Alignment. Operation(s) that can be applied to a single Row can be applied to a Group.


  • Locked Region: An un-modifyable set of cells in an Alignment Container or an Alignment. Locks can be set within a single Alignment or inherited from an Alignment Container.


  • Multi-Gene Alignment: an Alignment that contains Sequence(s) for multiple Gene(s) from different organisms on the Tree of Life.


  • Row: A single, horizontal segment of an Alignment Container which should logically contain at most one Alignment for a Sequence from a single gene for a given organism; however it can logically contain multiple sequences from different genes for a given organism.
  • rCAD Database:


  • Sequence: An ordered arrangement of Nucleotide(s) that are considered together as an immutable set.
  • Structural Relationship: Two or more Nucleotide(s) in a sequence interact to form a higher order interaction. A separate dictionary of biologically relevant structural relationships can be made available.
  • Student: A User who has no privileged access within the rCAD Database.


  • User: The generic definition for the role that represents an external human who interacts with the CAT UI. This role is subdivided based on privilege levels within an attached rCAD Database.


  • View: A visual rendering of content within the CAT UI. This content includes biological elements such as Alignment(s). Depending on the size of the content, the visual rendering may only contain a subset of the content (based on Context), and multiple visual renderings of the same content are possible.


  • Window: A software entity that encapsulates multiple Views and provides for a User to interact with the application.

Last edited Dec 10, 2008 at 9:06 PM by kjdoshi, version 21


No comments yet.