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Chromosome Aberration Analyzer (CAA) Completion Window
Input | ExampleThe test applet considers an input as "apparently incomplete" unless each color has at least one centromere and has exactly two apparent telomeres for each centromere. The interpretation of apparent incompleteness in the absence of a pan-telomeric probe is that the overall pattern indicates some failure of DSB free ends to rejoin or misrejoin and/or some cryptic chromatin segments too small to be seen. A systematic theory of apparent incompleteness has recently been developed and is partially incorporated into the test applet. If the input pattern is apparently incomplete, pressing any of the buttons will launch a dialog box which offers to open a Completion Window. Choosing "Yes" will open a new Completion Window with the mFISH pattern as input.
The methods currently employed by the completion window generate a family of complete patterns consistent with an incomplete mFISH pattern and a minimum number of "moves." There are three types of moves: M1(a, b), M2(a, b), and M3(a, b) where a and b are labels involved in the aberration.
- An M1(a, b) move adds a small fragment of label a to an apparent telomere end of label b.
- An M2(a, b) move adds a small, acentric fragment of the form (a::b)
- An M3(a, b) move anneals two separate fragments along apparent telomeres with labels a and b.
A minimal completion of an aberration is a complete mFISH pattern that can be obtained from the original aberration using a minimal number of moves.
More recent results, which incorporate the possibility of true incompleteness (especially in the case that M3 moves are involved), have not yet been implemented in the applet.The rules regarding valid input strings are the same as those for the Pattern Analysis window. To find a completion we require that the pattern be centromere complete, i.e. every chromosome involved in the aberration has a centromere in the final pattern.
Below is a sample completion window. The Minimal Move Sequences button lists all sequences of moves that complete the aberration in a minimal number of moves. Every centromere complete aberration admits a minimal completion and the list of move sequences is exhaustive.
The All Minimal Completions button lists all complete patterns generated by applying the move sequences in all possible ways to the initial pattern. The Minimal Completions with Obligate Cycle button lists all these completions along with the obligate exchange cycle of that completion.
Lastly, the Obligate Completions button lists only those completions with smallest obligate cycle.
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