SyntenyMapper v. 1.0
SyntenyMapper is a tool for the refinement of pre-computed syntenic regions through the identification of blocks of conserved gene order within. SyntenyMapper can be used on user-defined data on the Galaxy platform or on ENSEMBL Compara syntenic regions and orthologs. If you are interested in using SyntenyMapper on your own synteny data or want to use TrackMapper, a tool for the comparison of two genomes' features (in a .bed file format), you can install SyntenyMapper and its tools from the Galaxy ToolShed. If you have not installed a Galaxy instance on your local server or machine, you can get it here. You can then install SyntenyMapper from Galaxy by searching for "synteny-mapper" in the Tool Shed.
If you are unfamiliar with Galaxy, please follow these instructions to install the framework and SyntenyMapper:
| 1) | Download Galaxy. |
| 2) | Create an Admin user following this tutorial. |
| 3) | Enable automatic tool dependency installation. To do this, enter the folder of the Galaxy installation (termed 'galaxy-dist'), and open the file universe_wsgi.ini. Remove the comment sign # in the line tool_dependency_dir= and name a location for installation of tool dependencies. |
| 4) | Start galaxy. To do this execute the run.sh file in 'galaxy-dist'. Open your browser and go to http://127.0.0.1:8080/admin. Congratulations! You have now installed Galaxy with Admin rights. |
| 5) | Browse tools via Search and browse Tool sheds and choose the tool shed. Now you can search for 'synteny_mapper', choose preview and install followed by install to Galaxy and install the tool for your local Galaxy framework. If you enable automatic dependency installation, Circos and R will be installed automatically and you can start using the tool at once. |
We suggest to use synteny and orthology information from ENSEMBL Compara if you do not have your own sources. ENSEMBL Compara's current version provides syntenic region information only for a limited number of species pairs. The pre-calculated SyntenyMapper results for these, including visualizations for all syntenic regions, can be accessed below.
Get pre-calculated SyntenyMapper results here.
Command-line version
Download source code here.
You can directly run the provided jar-File in a Unix command line with the following parameters: java -jar syntenyMapper.jar synteny_outputFile orthology_outputFile outputFile1 outputFile2 species1 species2 if you want to download the files with syntenic regions and orthologous genes from ENSEMBL.
or java -jar syntenyMapper.jar syntenyFile orthologyFile outputFile1 outputFile2 for custom input files (format described below).Syntenic region file:
First two comment lines (marked by a leading #) in this file should name #Species1: and #Species2:, respectively. IDs should consist of five digits. The format should be in the following style (tab-separated):| #ID | Chromosome_species1 | Start_species1 | End_species1 | Chromosome_species2 | Start_species2 | End_species2 | Direction_species2 |
Orthologous genes file:
In this file each line corresponds to a single gene, and orthologs should have the same ID.| #ID | ENSEMBL_ID | Name | Chromosome | Start | End | Direction | Identity | Species |