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SyMAP Collinear |
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Details of Collinear sets
Using the
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In the image on the right, two different sets are shown (green highlighted hits is the 1st set,
pink is the 2nd). They were broken up by a gene on each chromosome
that do not have a hit.
In the image on the right, all genes in both sets are on the same strand. In the image below, all genes are on opposite strands.
The collinear set algorithm does not consider the amount of overlap of the hit to a gene, or the similarity of the hit sequences. |
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The following are examples of interpreting the 2D view:
| Sometimes a hit looks like it overlaps a gene, but the gene is actually in the gap, so it is not hit. This is illustrated on the right, where the 3 genes at the bottom appear hit by the red hit wire, but in fact are spanned by the gap gray area. Note that the hit popup shows it is a g0 hit (hits no genes). |
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The image on the right shows one collinear set with 6 brown hit wires that are not part of the set. The following
explains them, using the symbols g0 (hits 0 genes), g1 (hits 1 gene), g2 (hits paired genes, at
least one on each chromosome).
As shown earlier, sometimes two genes look as one, so the |
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Release v5.5.6
The collinear algorithm was improved for release v5.5.6.|
Pre-v5.5.6 gave obviously wrong results if a gene from the hit numbered project
(the hits are numbered along the alphabetically lesser project name) was part of two different collinear sets. An example
is on the right.
In my test sets, this happened a few times between Arabidopsis, Brassica rapa, and cabbage, but none for my partial mammalian test set of humans, chimps, mouse and rabbit. |
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| Referring to the image on the right (from the demo), pre-v5.5.6 called this one collinear set, ignoring the extra embedded gene 4941.b; v5.5.6 breaks it into two sets due to gene 4941.b (as shown in the image). |
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