diff --git a/docs/source/conventions/normalization.rst b/docs/source/conventions/normalization.rst index 0b4d12c2..170a8af2 100644 --- a/docs/source/conventions/normalization.rst +++ b/docs/source/conventions/normalization.rst @@ -216,5 +216,12 @@ will be selected by meeting the following ordered criteria. 2. The adjoined sequence accessions are equal or in ascending lexicographical order. 3. The defined adjoined sequence coordinates are in ascending numerical order. -When adjacencies are used in the context of a :ref:`DerivativeMolecule`, the traversal -direction is definitional and must be specified using a :ref:`TraversalBlock`. \ No newline at end of file +When adjacencies are used in the context of a :ref:`DerivativeMolecule`, the orientation +is definitional and must be specified using a :ref:`TraversalBlock`. + +.. figure:: ../images/ex_adjacency_orientation.png + + **The same pair of adjacencies can produce significantly different derivative molecules + depending on orientation.** In the top example, a 100-base sequence is deleted and + replaced by a 1000-base inverted sequence. In the bottom example, a 100-base inverted + sequence is inserted, and a 1000-base sequence is duplicated. diff --git a/docs/source/images/ex_adjacency_orientation.png b/docs/source/images/ex_adjacency_orientation.png new file mode 100755 index 00000000..c74dd580 Binary files /dev/null and b/docs/source/images/ex_adjacency_orientation.png differ