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Collinear sets Hit popup 3-chr conserved    2D    Queries

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Collinear sets

Using the Hit Filter, or right click in the hit region, set the highlighting for Collinear Sets. As shown below, the number of highlighted collinear hits and sets will be shown in the Information box.
Collinear Sets

In the image on the right, two different sets are shown where the pink highlighted hits is the 1st set, green is the 2nd; these are Color Wheel Highlight1 and Highlight2 colors. The sets were broken by an extra gene on Human Chr01.

A collinear set either has all genes to the same strand (+/+, -/-) or different (+/-, -/+). In the image on the right, all genes in both sets are on different 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.

Sometimes a hit looks like it overlaps a gene, but the gene is actually in the gap of a clustered hit, so is not a gene hit.

2 Collinear Sets

The image below shows a collinear set of 4 genes and 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).

1g1Ignored, not part of the set since it does not hit paired genes.
2g0Ignored.
3g1Ignored since the same gene has a hit to a paired gene.
4g0Ignored.
5g1This ends the set since it does not hit a paired gene.
6g2This could start a new set, but is not followed by another paired gene.

Sometimes two genes look as one, so the Sequence Filter Gene Delimiter option is important to view these.
Collinear Highlight and Gene Lines

Collinear hits

Hit popup

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Default view:

Merge

2D Hit Merge In the merge view, hits with gap<=0 are merged with the hit they overlap with.

The numbered hits are no longer 1-to-1, i.e. they do not necessarily align to each other like they do in the un-merged view.

Totals are provided for the Len and Gap.

The merge view corresponds better to the visual view on the 2D track.

The existence of the Merge is a quick indication that there are overlapping hits.

Order

2D Hit Order As stated above, each numbered hit corresponds to the same number in the opposite list, e.g. the two #1 aligns. An # on the far right implies that the order numbers are not sequential.

The Order option produces another popup where the target list is sorted by the # column, and the coordinates are no longer sorted.

The existence of the Order is a quick indication that there are disordered hits.

3-chr conserved

Both the Chromosome Explorer and Queries allow viewing results from 3 chromosomes.

Chromosome Explorer

The Dot plot can show 3 chromosomes, as illustrated on the right (click image for a better view).

 

Selecting 2D brings up the 3-track view, as discussed below.

dotplot

2D: The Sequence Filters for the reference track will have an extra section of filters as shown below.

g2x2The genes conserved across the 3-chromosomes are highlighted along with the hit-wires.
g2x1The genes conserved on ONLY one chr-pair are highlighted along with the hit-wires.
ShowOnly the g2x2 or g2x1 hit-wires will be shown.
sequence filter reference

The g2 implies the hit has a gene on both ends, and the x2 indicates it exists for both sets of chromosome pairs, the x1 indicates it exists for just one. When either g2x2 or g2x1 is selected, this algorithm is run to compute the values; it is only computed on the visible set.

There are two issues confusing the results:

g2xN Notice that when this feature is used along with the Sequence Filter of Show Gene#, the Gene# is only shown for the highlighed genes.

Caveats of display: Nothing is refreshed or recalulated!

Caveats of algorithm:

Queries: There is no query filters that give equivalent results.

Queries

→ For a query result, Report is only way to view more than two species in a query row.
→ As shown here, it is possible to bring up the 2D display with 3 chromosomes from the query table.

Select two rows with the following requirements: (1) Each row must have two genes. (2) There must be a shared gene.

Different species
Select 2 rows

Select View 2D with either the Region and Collinear options. The image on the right used the Collinear options.

Same species
Select 2 rows

Atha will be the reference since Gene# 5468 is listed in both rows, and Brap chromosomes 7 and 9 will be on its left and right. 2D image not shown.

report A.thal ref
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