SyMAP Demo

Demo and Synteny Results

The first section provides results from the supplied demo, which is used by System Guide in discussion of running the demo.

The second section describes synteny results using the different options; it uses a chromosome from Arabidopsis thaliana and one from Brassica rapa.

Demo Results

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

Two complete genomes

Draft

Self-synteny

symap.log

Two complete genomes: Demo-Seq to Demo-Seq2

Click an image to view a closeup.

The demo that is provided with the SyMAP tarball has the projects demo_seq, demo_seq2 and demo_draft.

The project demo_draft..demo_seq2 is created with ordered contigs, as described in Draft.

This section discusses the demo_seq to demo_seq2 synteny, which represent complete genome sequences.

There are a variety of options, as discussed in Pair Parameters. The following shows the Dot Plot and Summary using the following:

Cluster Algo1 (original modified) or Cluster Algo2 (exon-intron): The second is recommended when there is good gene annotation provided; it cannot be used for self-synteny.
Synteny Original or Synteny Strict: The second is recommended for complete genome sequence; it does not perform well for draft.

Cluster Algo1 (original modified) and Synteny Original

Cluster Algo2 (exon-intron) and Synteny Strict

There is very little difference between the Dotplots. The differences are more pronounced on the Chromosome Explorer 2D and Queries. The difference in the synteny algorithm are obvious on the more complicated examples, as shown in Synteny.

Draft: Demo-Draft to Demo-Seq2

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.


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.

Self-synteny: Demo-Seq

`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).

symap.log

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

The parameters selected are:

 Use previous 2 MUMmer files 17-Aug-25 13:45   CPUs: 2
 Cluster Algo1 (modified original) or Cluster Algo2 (exon-intron)
     Number pseudo
  Synteny Original
     Same orient

The 2 MUMmer files indicates the chromosome were not split and Concat was used. These two facts along with the number of CPUs can make subtle differences in the output.

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 from 2 files
   Scan files to cluster and filter hits
    11,000 Total cluster hits
     6,816 Filtered hits to save
   Finding Collinear sets
       717 Collinear sets
   Assign pseudo genes
       700 Pseudo Demo_Seq     485 Pseudo Demo_Seq2
Finish clustering hits               8s

Finding synteny for demo_seq and demo_seq2
        23 Blocks   Orient: 13 Same   10 Diff
Finish Synteny                       2s

Algo1 verbose


Loading annotations
    10,108 demo_seq genes
    10,137 demo_seq2 genes
   Scan files to create candidate genes from hits
    14,058 scanned PROMER demo_seq_cc.demo_seq2_f1.mum
     5,947 scanned PROMER demo_seq_cc.demo_seq2_f2.mum
    20,005 Total scanned hits from 2 files
   Scan files to cluster and filter hits
     6,923 clustered demo_seq_cc.demo_seq2_f1.mum
     4,077 clustered demo_seq_cc.demo_seq2_f2.mum
    11,000 Total cluster hits
Filter hits
     8,556 for demo_seq
     7,350 for demo_seq2
     6,816 Filtered hits to save
Save results
   Save filtered hits
   Save hit to gene
     6,564  (6,375) for demo_seq
     6,564  (12,749) for demo_seq2
   Finding Collinear sets
       717 Collinear sets
     1,969 Updates
   Finish Collinear            0s
   Assign pseudo genes
       700 Pseudo Demo_Seq     485 Pseudo Demo_Seq2
Finish clustering hits               8s

Finding synteny for demo_seq and demo_seq2
     6,816 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
           Collinear sets not in blocks (size: #sets):  2: 21  3: 1
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    Raw hits 20,005    Files 2                             .
     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_cc.demo_seq2_f1.mum  Hits 14,058 (EQ 2,893 NE 11,165)
        3,038 Clusters chr1-chr3   Both genes  3,022   One gene     13   No gene      3
          490 Clusters chr1-chr5   Both genes    484   One gene      5   No gene      1
   Load demo_seq_cc.demo_seq2_f2.mum  Hits 5,947 (EQ 2,366 NE 3,581)
          429 Clusters chr3-chr3   Both genes    417   One gene      7   No gene      5
          802 Clusters chr3-chr5   Both genes    790   One gene      9   No gene      3
   Final totals    Raw hits 20,005    Files 2
     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
     1,714 Updates
   Finish Collinear            0s
   Assign pseudo genes
        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
           Collinear sets not in blocks (size: #sets):  2: 15  3: 1
Finish Synteny                       2s

Synteny Results

The following is from comparing Arabidopsis thaliana chromosomes 1 and 2 with Brassica rapa chromosomes 1 and 7. The Clustering hits Algo2 (exon-intron) was used in all cases.

Original vs Strict: Both allow a mix of inverted and non-inverted hits in a block, but Strict only allows small inversions within a non-inverted block and vice-versa (unless Merge is used). The Strict blocks tend to not have the tails of dots that have bigger gaps.
Original	Strict
Original chr1&chr7	Strict chr1&chr7

Orient: This requires all hits in a block to be in the same orientation. This options fits with what some other software packages consider 'synteny'.
Original Orient chr1&chr7	Strict Orient chr1&chr7

Merge Overlap: Only overlapping blocks can be merged. This will have little effect if Orient has been used since mixed blocks cannot be merged.
Original Merge Overlap chr1&chr7	Strict Merge Overlap chr1&chr7

Merge Close: Blocks that are close can be merged.
Original Merge Close chr1&chr7	Strict Merge Close chr1&chr7

Go to top

Email Comments To: symap@agcol.arizona.edu