Try CSynth

A recent version of CSynth is now available to try out yourself.
You can view a simple, publicly-available dataset derived from yeast, or upload and visualise your own conformational data generated “in-house”.

 

Yeast, demonstration dataset (Crick model):

This data, derived from a study in fission yeast (S. pombe), shows conformational changes on the right arm of chromosome II during mitosis and interphase as well as the patterns of condensin binding sites. The data was modelled at the Crick Institute and is published in Nature Genetics (Kakui et al, 2017), and available at GEO (acc. GSE94478)

Launch CSynth

All the files used in this dataset can be downloaded at: crick_data_files.zip

 

Upload your own dataset:

When uploading data to create a project the first dataset would be a file of experimentally-derived, contact information. This can be in either ‘.contacts’ format or ‘.normMatrix’ format (NOTE: upon upload, the latter format is converted to a binary equivalent, ‘.bintri’, format to improve CSynth performance). The following guide should be used to ensure any uploaded data is in a compatible format:

Contacts Format: CSynth accepts a number of data formats. The contacts are recorded using a simple, 3-column file format, encoding the interaction between two positions on the chromosome (first 2 columns) and the strength of that interaction (last column). The expected file extension is ‘.contacts’. The contacts are restricted to cis interactions and each file should contain data relating to just one chromosome.
A typical example would look like:

normMatrix Format: This matrix format enables whole genome contact data to be stored in relatively compact form.
Download an example dataset (zipped .normMatrix format)

BED Format: The contacts file above is the minimum requirement for viewing data using CSynth and can be visualised without any further accessory files. It is sometimes useful however to highlight different regions of the genome under investigation using either text labels or by colouring the DNA backbone. Both of these can be achieved using an accessory, BED format identifying the regions to be highlighted.
This file records the name of the reference sequence, and the start  and end of the highlighted region in the first three columns. Any labels for the region are recorded in the fourth column and the desired colour (RGB value) for the region is recorded in the ninth column. An example of this file format is given below:

More details concerning BED format can be found at UCSC: file FAQ

WIG Format:
This data format allows the visualisation of quantitative data (e.g. from ChIP-Seq) on the chromosome where the diameter of the ribbon increases proportionally to the value in the wig file.
More details concerning WIG format can be found at UCSC: file FAQ

XYZ Format:
An existing conformational 3D model can be described using XYZ format and is useful to allow comparisons with the Hi-C contact data or the results of CSynth folding generated from Hi-C. An example of the XYZ file format is given below:

Data upload:
Data can be uploaded at:  CSynth Projects