SyMAP Demo

Draft

The demo was created from real data >15 years ago, and is VERY obsolete - it is strictly for demonstration.
This is used by System Guide.

Demo-Seq to Demo-Seq2

Available

Dot plot

Chromosome Explorer

Queries

Algo1 vs Algo2

	Click an image to view a closeup.
This document shows the different views for the `Demo-Seq` to `Demo-Seq2` alignment. When synteny has been computed for the demo, the Available Syntenies table will have a check (✓), signifying that the synteny is available for viewing. The cell will be highlighted green, which will enable the viewing buttons, e.g Dot Plot.

Click Dot Plot and you will see the dot plot shown here. By clicking and/or selecting regions you can zoom into certain regions and bring up detailed views of the alignments. The ? button links to the online documentation that provides full information on the functions. The (i) button links to a popup with some brief information.
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Click the Chromosome Explorer button and you will see the display shown on the right, but no circle. The top left chromosome icon will have its number highlighed in a red box; this indicates it is the default reference chromosome. Click on the icon body for `Demo-Seq2` 1 and 3 (i.e. chr1 and chr3) to see the Circos-style³ view shown on the right. The ribbons represent synteny blocks.
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Click the 2D button to see a side-by-side view of the same chromosomes. Note that the reference is in the middle. The lines between chromosomes indicate the individual clustered hits.
By dragging the mouse over a region of one chromosome, the display will zoom in on that region, as shown in the image on the right. The exons for individual genes can be seen in the center of each sequence track. The length of the hit is shown on the inner boundary of the each chromosome segment. There is a Sequence Filter for Annotations. This will show the annotation as shown on the right, but it must be zoomed in close enough. Alternatively, as long as the view is zoomed enough to see the individual exons, right-click on a gene for a popup of the annotation.
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Click the Queries button. This brings up the query window in Overview mode. Click the Query Setup option on the left-hand side and you will see the corresponding window:
Using the query setting from above produced the results table shown on the right. Columns can be changed, sorted and moved.

Algo1 versus Algo2

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The following show the summary when the Synteny Clustering was run with Algo1 versus Algo2.

Self-synteny of Demo-Seq

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`Demo-Seq` has been run against itself, resulting in the Dot Plot shown on the lower right. There are a few off-diagonal blocks, which may indicate repetitiveness (but these blocks are probably too small to be meaningful).
Click to view summary

Demo-Draft to Demo-Seq2

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The `Demo-draft` was run against the `Demo-Seq2` with its order_against parameter set to `Demo_Seq2`. The resulting dot plot is shown on the right. Note that the 43 contigs are ordered, but still fragmented.
Click to view summary

When the ordering algorithm is run, it creates a new project called `Demo-Draft.Demo_Seq2`, where the 43 contigs are written into three chromosomes; the first two correspond to chr1 and chr3 of `Demo_Seq2`, and chr0 contains the contigs that do not align. The new project `Demo-Draft.Demo_Seq2` was aligned with `Demo_Seq2`, resulting in the dot plot shown on the right.
Click to view summary

symap.log

The following 4 sections show the contents of the logs/<proj-to-proj>/symap.log file:

For all 4 variations, the first two lines are:


>>> SyMAP v5.6.8  (1-June-25)    Running Java v20.0.1 on 24-May-25 15:28:45 <<<
>>> demo_seq to demo_seq2    Verbose (or !Verbose)

The parameters selected are:

Cluster Algo1 (modified original) or Cluster Algo2 (exon-intron) Number pseudo Synteny Same orient

The last 6 lines are the Summary (not shown).

Algo1 !verbose


Start calculating cluster hits for demo_seq and demo_seq2
   Alignment files in data/seq_results/demo_seq_to_demo_seq2/align/
   Scan files to create candidate genes from hits
    20,005 Total scanned hits
   Scan files to cluster and filter hits
    11,000 Total cluster hits
     6,841 Filtered hits to save
   Finding Collinear sets
       717 Collinear sets
   Assign pseudo genes
       703 Pseudo Demo_Seq     478 Pseudo Demo_Seq2
Finish clustering hits               8s

Finding synteny for demo_seq and demo_seq2
        23 Blocks   Orient: 13 Same   10 Diff
Finish Synteny                       3s

Algo1 verbose


Start calculating cluster hits for demo_seq and demo_seq2
   Alignment files in data/seq_results/demo_seq_to_demo_seq2/align/
Loading annotations
    10,108 demo_seq genes
    10,137 demo_seq2 genes
   Scan files to create candidate genes from hits
     3,596 scanned PROMER demo_seq_f2.demo_seq2_f2.mum
     2,423 scanned PROMER demo_seq_f2.demo_seq2_f1.mum
    11,635 scanned PROMER demo_seq_f1.demo_seq2_f1.mum
     2,351 scanned PROMER demo_seq_f1.demo_seq2_f2.mum
    20,005 Total scanned hits
   Scan files to cluster and filter hits
     2,296 clustered demo_seq_f2.demo_seq2_f2.mum
     1,834 clustered demo_seq_f2.demo_seq2_f1.mum
     5,089 clustered demo_seq_f1.demo_seq2_f1.mum
     1,782 clustered demo_seq_f1.demo_seq2_f2.mum
    11,001 Total cluster hits
Filter hits
     8,557 for demo_seq
     7,388 for demo_seq2
     6,842 Filtered hits to save
Save results
   Save filtered hits
   Save hit to gene
     6,591  (6,402) for demo_seq
     6,591  (12,809) for demo_seq2
   Compute and save hit#
   Compute and save gene numHits
   Finding Collinear sets
       717 Collinear sets
     1,969 Updates
   Finish Collinear            0s
   Assign pseudo genes
          469 Pseudo Demo_Seq chr3     Genes  5,775   Start  6,000
          234 Pseudo Demo_Seq chr5     Genes  4,333   Start  5,000
          257 Pseudo Demo_Seq2 chr1    Genes  5,573   Start  6,000
          221 Pseudo Demo_Seq2 chr3    Genes  4,567   Start  5,000
       703 Pseudo Demo_Seq     478 Pseudo Demo_Seq2
Finish clustering hits               8s

Finding synteny for demo_seq and demo_seq2
     6,842 Total hits
         4 group-x-group pairs to analyze
           12 Blocks chr3-chr1     Orient:  Same   8   Diff   4
            2 Blocks chr3-chr3     Orient:  Same   1   Diff   1
            1 Blocks chr5-chr1     Orient:  Same   0   Diff   1
            8 Blocks chr5-chr3     Orient:  Same   4   Diff   4
        23 Blocks   Orient: 13 Same   10 Diff
Finish Synteny                       3s

Algo2 !verbose


Start calculating cluster hits for demo_seq and demo_seq2
   Alignment files in data/seq_results/demo_seq_to_demo_seq2/align/
   Final totals
     4,759 Clusters  Both genes    4,713   One gene       34   No gene       12
     6,883 Filtered  Both genes    6,883   One gene    3,263   No gene    2,453   Pile hits 1,167
   Finding Collinear sets
       635 Collinear sets
   Assign pseudo genes
        37 Pseudo Demo_Seq     21 Pseudo Demo_Seq2
Finish clustering hits               7s

Finding synteny for demo_seq and demo_seq2
        19 Blocks   Orient: 9 Same   10 Diff
Finish Synteny                       2s

Algo2 verbose


Start calculating cluster hits for demo_seq and demo_seq2
   Alignment files in data/seq_results/demo_seq_to_demo_seq2/align/
   Load genes for Algo2
      Demo_Seq2  [Avg Min Max] [Gene 2,968  120   89k] [Intron   430    1   87k] [Exon   294    3 4,935] Cov 46.5%
      Demo_Seq   [Avg Min Max] [Gene 2,575   63  508k] [Intron   373    1  501k] [Exon   379    1 6,153] Cov 57.8%
   Load demo_seq_f2.demo_seq2_f2.mum  Hits 3,596 (EQ 1,214 NE 2,382)
          802 Clusters chr3-chr5   Both genes    790   One gene      9   No gene      3
   Load demo_seq_f2.demo_seq2_f1.mum  Hits 2,423 (EQ 1,248 NE 1,175)
          490 Clusters chr1-chr5   Both genes    484   One gene      5   No gene      1
   Load demo_seq_f1.demo_seq2_f1.mum  Hits 11,635 (EQ 1,645 NE 9,990)
        3,038 Clusters chr1-chr3   Both genes  3,022   One gene     13   No gene      3
   Load demo_seq_f1.demo_seq2_f2.mum  Hits 2,351 (EQ 1,152 NE 1,199)
          429 Clusters chr3-chr3   Both genes    417   One gene      7   No gene      5
   Final totals
     4,759 Clusters  Both genes    4,713   One gene       34   No gene       12
     6,883 Filtered  Both genes    6,883   One gene    3,263   No gene    2,453   Pile hits 1,167
   Compute and save hit#
   Compute and save gene numHits
   Finding Collinear sets
       635 Collinear sets
     1,714 Updates
   Finish Collinear            0s
   Assign pseudo genes
           23 Pseudo Demo_Seq chr3     Genes  5,775   Start  6,000
           14 Pseudo Demo_Seq chr5     Genes  4,333   Start  5,000
            6 Pseudo Demo_Seq2 chr1    Genes  5,573   Start  6,000
           15 Pseudo Demo_Seq2 chr3    Genes  4,567   Start  5,000
        37 Pseudo Demo_Seq     21 Pseudo Demo_Seq2
Finish clustering hits               7s

Finding synteny for demo_seq and demo_seq2
     4,759 Total hits
         4 group-x-group pairs to analyze
           12 Blocks chr3-chr1     Orient:  Same   8   Diff   4
            1 Blocks chr3-chr3     Orient:  Same   0   Diff   1
            1 Blocks chr5-chr1     Orient:  Same   0   Diff   1
            5 Blocks chr5-chr3     Orient:  Same   1   Diff   4
        19 Blocks   Orient: 9 Same   10 Diff
Finish Synteny                       2s

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Email Comments To: symap@agcol.arizona.edu