CHROnicle » SynChro

SynChro

SynChro: reconstruction and visualization of Synteny blocks along Chromosomes.

Overview:

SynChro is a tool designed to identify conserved synteny blocks. It reconstructs synteny blocks between pairwise comparison of multiple genomes. The reconstructed synteny blocks may overlap each other, be included in one another or duplicated due to micro-rearrangements. SynChro provides the user with a rich set of outputs including various data visualization possibilities (dotplots, chromosomal paintings and detailed synteny maps, which allow local as global views of the synteny blocks) and analysis tools (to compare the different sets of synteny blocks). Its main advantages are the followings

  • No need for pre-computed families of orthologs. A simple list of ordered genes and their amino-acid sequences is required as input (which can be EMBL or GenBank files).
  • Only a single parameter to set up: the block stringency (Delta).
  • It is fast enough to be run on large eukaryotic genomes (the Human/Mouse comparison takes less than 30 minutes on a Desktop computer).

Downloads

1. If it is the first time you use/download a CHROnicle program, you need to download the CHROnicle architecture, which contains toy examples as well as scripts that converts EMBL and GenBank files into the expected SynChro input format.

2. Then you need to download the SynChro program and to add it to your CHROnicle/Programs/ directory:

Please take a look at the README file for usage instructions.

Quick start

(notice that the different scripts and programs are all conserved in the CHROnicle/Programs/ directory.)

1. Create a Cladename directory such as CHROnicle/CladeName/. See for example the CHROnicle/Yeast/ directory.

2. Fill the directory CHROnicle/CladeName/01Genomes/ with your 'well-formatted' genomes.

You can format input files from EMBL genome files. For instance, in the CHROnicle/Programs/0Convert2InputF/ directory, if you type the following command:

./ConvertEMBL.py Yeast CandidaTropicalis CATR

this will create, in the directory CHROnicle/Yeast/01Genomes/, the three input files associated to the C. tropicalis (abbreviated as CATR) genome (from the EMBL files present in the directory CHROnicle/Yeast/00rawGenom/CandidaTropicalis/)

or

format input files from GenBank genome files. For instance, in the CHROnicle/Programs/0Convert2InputF/ directory, if you type the following command:

./ConvertGbk.py Vertebrate GallusGallus GALG

this will create, in the directory CHROnicle/Vertebrate/01Genomes/, the three input files associated to the G. gallus (abbreviated as GALG) genome (from the GenBank files present in the directory CHROnicle/Vertebrate/00rawGenom/GallusGallus/).

Look at the CHROnicle/Programs/0Convert2InputF/README_Convert2InputF.txt file for a description of how Convert.py files work and a detailed description of required input formats (if you do not have EMBL, GenBank or Fasta files).


3. Compute synteny blocks with SynChro. For instance, in the CHROnicle/Programs/1SynChro/ directory, if you type the following command:

./SynChro.py Yeast 0 2

this will reconstruct synteny blocks between all yeast genomes present in your input set of genomes (in the directory CHROnicle/Yeast/01Genomes/). The second numerical argument is the value of delta (here 2). If you want to compute synteny blocks (for delta=2) only for some pairwise comparisons of genomes in your dataset, you just have to change the first numerical argument 0 into 1 (you will be prompted to say which genomes you want to compare). Notice that if you add one new genome, you can re-launch SynChro for all genomes (with 0 as first argument), as synteny blocks already computed are not re-computed, only the pairwise comparisons involving the new genome will be done.


4. Generate a table summarizing the properties of synteny blocks from the different pairwise comparisons. For instance, in the CHROnicle/Programs/1SynChro/Summary/ directory, if you type the following the command:

./Summary.sh Yeast 2

this will summarize the different properties of the yeast synteny blocks (here with delta=2) in the file CHROnicle/Yeast/11Blocks/Delta2/SummaryY2.txt

5. Plot some of these block properties. For instance, in the CHROnicle/Programs/1SynChro/Summary/ directory, if you type the following command:

./PercentGenomefDiv.sh Yeast 2

this will plot the percentage of the genome comprised within synteny blocks as a function of the average divergence between orthologous proteins.

6. Reconstruct families of syntenic homologs. For instance, in the CHROnicle/Programs/1SynChro/ directory, if you type the following command:

./InterOrtho.py Yeast 2 80

this will provide a list of families of syntenic homologs (with a average of similarity bigger than 80%) for the set of genomes present in the CHROnicle/Yeast/01Genomes/(families are in the CHROnicle/Yeast/12OrthFamilies/Delta2/ directory).

Contact

For questions, comments, or suggestions feel free to contact Guénola Drillon.

References

  • Drillon G, Carbone A and Fischer G (2014) SynChro: A Fast and Easy Tool to Reconstruct and Visualize Synteny Blocks along Eukaryotic Chromosomes. PLoS ONE 9 (3): e92621. doi:10.1371/journal.pone.0092621
  • Drillon G, Carbone A and Fischer G (2011) Combinatorics of chromosomal rearrangements based on synteny blocks and synteny packs. Journal of Logic and Computation. doi: 10.1093/logcom/exr047 (pdf)

Last Update January 2015