The config file indicates which syntenic data file to open, along with optional annotation tracks. If no annotation tracks are included, the config file looks like this:


tracks 0

For data sets including annotation tracks, the config file lists each annotation file along with a tag for the track.


tracks 3

./rhizopus_trna.txt tRNA

./rhizopus_ltr.txt LTR

./rhizopus_regions.txt region

Config File

Data files can be comma-separated or tab-separated. The files included with the above executables are of the latter type. The location of blank lines is important!

For files containing the information about the syntenic blocks, such as for this one, the top part contains information about the genomes and chromosomes. Each chromosome is listed with a tag and length. For conservation within a single genome, only one genome and list of chromosomes is included, such as in this data set.

genome Stickleback

chromosomes 22

chrI 28185914

chrII 23295652

chrIII 16798506


genome Tetraodon

chromosomes 21

chr1 16827091

chr2 19247847

chr3 14679700


The second part of the file contains information about the syntenic blocks. For each block, the first line includes: source chromosome tag; block start coordinate; block end coordinate; block orientation; destination chromosome tag; destination block start coordinate; destination block end coordinate; destination block orientation; conservation strength of blocks; number of conserved genes in block. Following this information, there is a line for each conserved gene that includes: gene start coordinate; gene end coordinate; gene orientation; destination gene start coordinate; destination gene end coordinate; destination gene orientation; conservation strength of genes. Each gene pair can also include gene tags, such as in this data file.

chrI 6774976 6785031 +1 chr10 9280732 9287089 +1 0.558624 25

6774976  6775170 +1 9280732  9280926 +1 0.634021

6775392  6775576 +1 9281133  9281317 +1 0.619565

6775628  6775794 +1 9281335  9281501 +1 0.60241

6775832  6776093 +1 9281501  9281762 +1 0.651341

Annotation tracks files contain a list genomic features, where each line contains: chromosome tag; feature start coordinate; feature end coordinate; an optional tag (which is currently not used in the system). The rhizopus data set contains several of these, such as for the location tRNA. Up to four annotation tracks can be included.

7    613081    613175    anticodon=TAT;type=Ile

7    1428707    1428778    anticodon=TTG;type=Gln

7    1548833    1548905    anticodon=CTG;type=Gln

7    1729193    1729274    anticodon=AGA;type=Ser


Data Format


The zip files below contain an executable, config file, and sample data sets. The config file must be in the same directory as the executable. The config file can be modified to point to any data on the local harddrive.

Two config files and associated data sets are included in the zip files. The default config.txt is set to load the stickleback-pufferfish data, and the config_rhizopus.txt loads the rhizopus data set that also contains three annotation tracks (LTR, tRNA, and regions). The application will read the file named config.txt.

executables (1200x800 resolution):

full screen executables:

About the data...

The rhizopus data set is courtesy of Dr. Li-Jun Ma, and the stickleback-pufferfish data is courtesy of Dr. Manfred Grabherr. Both scientists are at the Broad Institute.