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Examples of DNA Components

DNA Components

Key

DCØ – DnaComponent w/o type, w/o sequence
DCt – DnaComponent w/ type
DCs – DnaComponent w/ sequence
DCst - DnaComponent w/ sequence and type
SAposN – SequenceAnnotation w/ position coordinates [N- ordinal for notation only]
SArpN – SequenceAnnotation w/ relative position (precedes)
SArpØ – SequenceAnnotation w/ relative position (terminal SA)
Col - Collection


Object Structure
Each example below is a valid SBOL structure


A. Basic

Structure: DCst1

An example of basic structure would be Terminator (BBa_J61048)

Graphically a basic structure will look like the example shown below. At the top level there is a DNA component which includes the entire component with associated sequence. From the top level there is one annotation that spans bases 2 to 12 on the positive strand [+]. Finally the annotation has a reference to a second DNA component which is used to store the details of the annotation, this includes a description and what type it is, e.g a terminator.


B. Composite


In addition to the basic type shown above it is also possible to have multiple annotations specified as the following examples illustrates.

Structure:
DCst → SApos1 (DCst1)
        →  SApos2 (DCst2), …
        →  SAposN (DCstN)

This is an example of a composite part.

BBa_T9002 1..54  (BBa_R0040 [promoter])
                   → 63..74 (BBa_B0034 [RBS])
                   → 81..836 (BBa_C0062 [CDS])

                   → 870..949 (BBa_B0010 [terminator])
                   → 958..998 (BBa_B0012 [terminator])
                   → 1007..1061 (BBa_R0062 [promoter])
                   → 1070..1082 (BBa_B0032 [RBS])
                   → 1089..1808 (BBa_E0040 [CDS])
                   → 1817..1929 (BBa_J61048 [terminator])

Graphically we can depict a composite part in the following way. Note that this example also illustrates that part of the DNA Component is not annotated, i.e. section 10 to 17 although the actual DNA sequence is specified. Each of the two annotations also has a corresponding DNA component that leads to more information about the annotated part


C. Multi-tiered

The milti-tiered example shows that a design can be expressed as a hierarchy of annotated subparts. In this case we have a top level that include the complete design. Below the top level DNA Component is a single annotated section (2-22). This in turns has its own DNA Components that describe in more detail the annotated sections (In this case only one section). In addition, the second DNA Component has its own annotation and its own DNA Components that describe in more detail the annotated section 2-22.

In all cases, indexing starts at ONE and that DC Components of subparts are indexed with respect to the subpart DNA.




Structure:
DCst → SApos1 (DCst1 → SApos2 (DCst2 → SAposN (DCst)))

Example:
BBa_S04263 → 729..857 (BBa_B0015  [terminator]) → 1..80 (BBa_B0010 [terminator]))


                                             

D. Overlapping

There are many example of overlapping features on DNA, the classic example being an overlap between LacI and the RNA promoter region. This example shows that overlaps are easy to accommodate in SBOL.


Structure:
DCst → SApos1 (DCst1)
        →  SApos2 (DCst2), …
Example:
BBa_T9002 → 1..54 (BBa_R0040 [promoter])
                   → 1..19 (TetR 1 [operator]))



Examples for Stages
Sequence Design
  1. Template
  2. Annotated Sequence
  3. Collection
Assembly Planning
Characterization Results

Annotation Detail

a. Relative Position

b. Coordinate Position

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