Table 1
From: A consolidation algorithm for genomes fractionated after higher order polyploidization
(Consolidation algorithm) |
|---|
Input: diploid genome D, ancient (2k)-ploid genome P, gene set L |
Output: gene set L', each element of L' is a virtual gene shared between D and P, the set of the virtual genes forms a partition of D . |
1: for each chromosome c in the diploid genome do |
2: recentTerm ← undefined |
3: for each gene g on chromosome c do |
4: for each occurrence occ of gene g on the hexaploid genome do |
5: create new terminal unit newTerm, set link to previous terminal unit |
6: if newTerm is not the first terminal unit on its chromosome then |
7: turn the older terminal unit into non-terminal unit newNonTerm |
8: update links between terminal units |
9: set startPos(newNonTerm), rMin(newNonTerm), rMax(newNonTerm) |
10: end if |
11: recentTerm ← newTerm |
12: end for |
13: [rMin min , rMax max ] ← [g, g] |
14: currUnit ← newTerm |
15: termCount ←0 |
16: minStartPos ← undef |
17: while currUnit exists and termCount ≤ k and rMax max ≤ g do |
18: if currUnit is a terminal gene then |
19: termCount ← termCount + 1 |
20: rMin min ← min(rMin min , gene of currUnit) |
21: if rMin min ≥ gene of currUnit then |
22: minStartPos ← gene of currUnit |
23: end if |
24: end if |
25: if currUnit is a non-terminal unit then |
26: if rMax(currUnit) ≤ g then |
27: while prevUnit(currUnit) is non-terminal and rMax(prevUnit(currUnit)) ≤ g do |
28: merge prevUnit(currUnit) into currUnit |
29: update link to previous unit |
30: update startPos(currUnit), rMax(currUnit) and rMin(currUnit) |
31: end while |
32: if startPos(currUnit) exists and rMin min ≥ startPos(currUnit) then |
33: minStartPos ←startPos(currUnit) |
34: end if |
35: end if |
36: rMin min ← min(rMin min , currUnit.rMin) |
37: rMax max ← max(rMax max , currUnit.rMax) |
38: end if |
39: currUnit ← prevUnit(currUnit) |
40: end while |
41: add [minStartPos, g] to list of virtual intervals |
42: end for |
43: end for |
44: remove redundant intervals from list of virtual intervals to obtain a partition of D |