WormBase converter (original) (raw)
Introduction
Introduction
The WormBase Converter allows the conversion of any Gene ID into any other Gene ID.
You can convert a "WormBase ID", a "Gene/Transcript/CDS Sequence Name" or a "Gene Name" into a_"WormBase ID"_, a "Gene Sequence Name" or a "Gene Name". Moreover, if you don't known the ID used in a gene list or if the list is composed by more than one ID, the tool detects automatically the IDs.
This tool also allows the conversion between the WormBase releases. You can convert a Gene ID in a specific release (e.g. 170) into another release (e.g. 190 for a conversion, or 160 for a reverse-conversion). If you are not sure about the release used in a gene list, the program detects it.
Finally, you can save all conversions and results in different files.
Citation
If you use any of these tools, please cite the following article:
Engelmann et al. A comprehensive analysis of gene expression changes provoked by bacterial and fungal infection in C. elegans. PLoS One (2011) 6(5):e19055
Download & Installation
To install the program, just download the correct archive below and extract it on your computer.
Read the documentation of the folder "help" in the archive, or download it (link below), to know how to configure the program.
If you wish to use it on a Mac, take the "Sources" file. As explained in the manual, you will need to have Perl and Python on your own Mac.
The tool is easy to install and configure with wizards, and easy to use. A tutorial for a quick start is available. Nevertheless, you are strongly recommended to go to http://www.ciml.univ-mrs.fr/applications/WB_converter/ before downloading anything!
Important Note: Since this software was first released, Wormbase has extensively altered the architecture of its ftp site, and the file structure. We have not been able to modify WormBase converter to accommodate these changes. The stand-alone updating function no longer works. There are two solutions: to use WormBase converter in Client mode and connect to the CIML server as described at http://www.ciml.univ-mrs.fr/applications/WB\_converter/, or, if you need to use a local server, to download the WormBase releases package available below. The documentation has not been revised to take these changes into account.
WormBase converter Downloads
LOCAL version
The LOCAL version should be used on independant computers.
The program runs entirely on the same computer (conversion and updates).
CLIENT version
The CLIENT version should be installed on a client computer that will connect to a server.
The program runs on the computer, but updates are downloaded from the server.
CLIENT version (Administrator)
The CLIENT version (Administrator) is the same version than the CLIENT version but the user has a full access to the software, and can change the server settings.
The program runs on the computer, but updates are downloaded from the server.
SERVER version
The SERVER version must be installed on a server.
It centralizes the WormBase releases, and allows the update of the clients automatically.