Contents:
The demo was created from real data >15 years ago, and is VERY obsolete - it is strictly for demonstration.
Click any image to view an enlarged image.
Demo-Seq to Demo-Seq2
The following show the summary when the Synteny Clustering was run with Algo1 versus Algo2.
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
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The Demo-draft was run against the Demo-Seq2 with its order_against parameter set to Demo_Seq2.
The following 4 sections show the contents of the logs/<proj-to-proj>/symap.log file:
The first two lines of each is:
>>> SyMAP v5.6.1 (27-Jan-25) Running Java v17.0.11 on 27-Jan-25 11:47:49 <<<
>>> demo_seq to demo_seq2 Verbose (or !Verbose)
The last 6 lines are the Summary (not shown).
As is obvious, most of the "verbose" is during the cluster algorithm.
Algo1, !verbose
Cluster Algo1 (modified original)
Warning: 2 alignment files exist - using existing files
If not correct, remove data/seq_results/demo_seq_to_demo_seq2 and re-align.
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
6,816 Filtered hits to save
Finish load hits 154.10Mb 7s
Finding synteny for demo_seq and demo_seq2
18 Blocks
Wrote data/seq_results/demo_seq_to_demo_seq2/final/block.txt
Wrote data/seq_results/demo_seq_to_demo_seq2/final/anchors.txt
Finish Synteny 5s
Finding Collinear sets
717 Collinear sets
Finish Collinear 0s
Algo1, verbose
Cluster Algo1 (modified original)
Warning: 2 alignment files exist - using existing files ...
If not correct, remove data/seq_results/demo_seq_to_demo_seq2 and re-align.
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
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
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
Compute and save hit#
Compute and save gene numHits
Finish load hits 117.44Mb 6s
Finding synteny for demo_seq and demo_seq2
6,816 Total hits
4 group-x-group pairs to analyze
18 Blocks
Wrote data/seq_results/demo_seq_to_demo_seq2/final/block.txt
Wrote data/seq_results/demo_seq_to_demo_seq2/final/anchors.txt
Finish Synteny 5s
Finding Collinear sets
717 Collinear sets
1,969 Updates
Finish Collinear 0s
Algo2, !verbose
Cluster Algo2 (exon-intron)
G0 length scale = 0.5
Warning: 2 alignment files exist - using existing files
If not correct, remove data/seq_results/demo_seq_to_demo_seq2 and re-align.
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 3,263 One gene 2,453 No gene 1,167 Pile hits 7
Finish load hits 95.47Mb 6s
Finding synteny for demo_seq and demo_seq2
18 Blocks
Wrote data/seq_results/demo_seq_to_demo_seq2/final/block.txt
Wrote data/seq_results/demo_seq_to_demo_seq2/final/anchors.txt
Finish Synteny 2s
Finding Collinear sets
635 Collinear sets
Finish Collinear 0s
Algo2, verbose
Cluster Algo2 (exon-intron)
G0 length scale = 0.5
Warning: 2 alignment files exist - using existing files
If not correct, remove data/seq_results/demo_seq_to_demo_seq2 and re-align.
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 chr3-chr1 Clusters Both genes 3,022 One gene 13 No gene 3
490 chr5-chr1 Clusters 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 chr3-chr3 Clusters Both genes 417 One gene 7 No gene 5
802 chr5-chr3 Clusters Both genes 790 One gene 9 No gene 3
Final totals
4,759 Clusters Both genes 4,713 One gene 34 No gene 12
6,883 Filtered Both genes 3,263 One gene 2,453 No gene 1,167 Pile hits 7
Compute and save hit#
Compute and save gene numHits
Finish load hits 96.43Mb 6s
Finding synteny for demo_seq and demo_seq2
4,759 Total hits
4 group-x-group pairs to analyze
18 Blocks
Wrote data/seq_results/demo_seq_to_demo_seq2/final/block.txt
Wrote data/seq_results/demo_seq_to_demo_seq2/final/anchors.txt
Finish Synteny 2s
Finding Collinear sets
635 Collinear sets
1,714 Updates
Finish Collinear 0s
>> Summary for demo_seq to demo_seq2
4,759 hits
18 synteny blocks
4,747 gene hits
3,260 synteny hits
Complete Alignment&Synteny 10s
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