MizBee
A Multiscale Synteny Browser
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:
./fish.txt
tracks 0
For data sets including annotation tracks, the config file lists each annotation file along with a tag for the track.
./rhizopus.txt
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
Executables
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.