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Assembly points
Each assembly can be represented as a set of individual assembly points (links), and that is the view that CAMSA takes on the input scaffold assemblies. This approach is very flexible and allows for a very broad range of scaffold assemblies obtained from both in silico and in vitro techniques.
We say that a scaffold has two extremities: head and tail, which can be viewed as 3' and 5' extremities of this scaffold. Thus the forward oriented scaffold A
will be described as +A
and negatively oriented scaffold will be denoted as -A
. When no orientation of scaffold A
is given, it will be denoted simply as A
.
In our terminology, an assembly point is an evidence, that two scaffolds need to be placed together. We classify into 3 categories:
-
oriented
:p=(+A, +B)
two scaffolds are reported as adjacent, and orientation of both scaffolds is specified. In this case, the head of scaffoldA
is adjacent to the tail of scaffoldB
. -
semi-oriented
:p=(+A, B)
two scaffolds are reported adjacent, but the orientation of only a single scaffold is known. In other words, we know by which extremity scaffoldA
(head) has to be adjacent to the scaffoldB
, but we don't know which extremity of scaffoldB
(head or tail) will be involved withA
. -
non-oriented
:p=(A, B)
two scaffolds are reported adjacent, but the orientations of both scaffolds are not known.
Such view inspires us to include the notion of assembly point realization. For a given assembly point p
a realization is an oriented assembly point, that can be inferred from p
by setting orientation to unoriented scaffolds participating in it.
Example: given a semi-oriented assembly point p=(+A, B)
, there exist two realizations of it:
(+A, +B)
(+A, -B)
With this in mind, we note, that each oriented assembly point has exactly a single orientation: itself. Every semi-oriented assembly point has exactly 2 orientations (by two possible orientations of the unoriented scaffolds), and every non-oriented assembly point has 4 orientation.
Sergey Aganezov & Max A. Alkseyev, Computational Biology Institute, The George Washington University