Genomatix Software GmbH

Introduction

This task identifies GeneIds in genomes of different species that are orthologous to the GeneIds in the input. To identify orthologous GeneIds in a target species, the homology groups of ElDorado (background) are used.
Lists of orthologous GeneIds can be saved and can be used as input for other Genomatix programs like GeneRanker or GePS.

Parameters

Input
Input	You can eitther paste a list of GeneIds into the input field or upload a file with GeneIds. In both cases the GeneIds can be separated by commas, blanks, or new lines. If both fields are filled, the pasted GeneIds will be used.
Organism	Please select the correct organism for the input GeneIds; input GeneIds will only be searched in this species.
Target
Target species	The program searches the genomes of the species you select here for GeneIds which are orthologous to the GeneIds in the input file. Depending on the source organism only a certain selection of target organisms is available (i.e. orthologs can be searched only within vertebrates, plants, or insects respectively).
Output
Result	Here, you can edit the default name of the result file.
Email address	Here you can choose between two methods for receiving the results: Show result directly in browser window In this option the URL of the result is directly shown in your browser window. Warning: Please use this option only for analyses which can be performed in a short time. If the analysis takes longer than the timeout of the webserver, the connection will be terminated and you will receive an error message (e.g. "The document contained no data."). In this case, the results will not be available, please restart the analysis using the option below "Send the URL of the result to". Send the URL of the result via email In this option an email with the URL of the results will be sent to the user provided email address, when the analysis is finished. The results will be available for a limited time on our server. For details of how long your results will be kept please see the result-email. After that period they will be deleted unless protected in the project management! We recommend to use the email option for more than 500 input GeneIds.

Input

You can eitther paste a list of GeneIds into the input field or upload a file with GeneIds. In both cases the GeneIds can be separated by commas, blanks, or new lines. If both fields are filled, the pasted GeneIds will be used.

Organism

Please select the correct organism for the input GeneIds; input GeneIds will only be searched in this species.

Target

Target species

The program searches the genomes of the species you select here for GeneIds which are orthologous to the GeneIds in the input file. Depending on the source organism only a certain selection of target organisms is available (i.e. orthologs can be searched only within vertebrates, plants, or insects respectively).

Output

Result

Here, you can edit the default name of the result file.

Email address

Here you can choose between two methods for receiving the results:

Show result directly in browser window
In this option the URL of the result is directly shown in your browser window.
Warning: Please use this option only for analyses which can be performed in a short time.
If the analysis takes longer than the timeout of the webserver, the connection will be terminated and you will receive an error message (e.g. "The document contained no data."). In this case, the results will not be available, please restart the analysis using the option below "Send the URL of the result to".
Send the URL of the result via email
In this option an email with the URL of the results will be sent to the user provided email address, when the analysis is finished.

The results will be available for a limited time on our server. For details of how long your results will be kept please see the result-email. After that period they will be deleted unless protected in the project management!

We recommend to use the email option for more than 500 input GeneIds.

Output

1. Analysis Parameters

2. Statistics of GeneIds

Note: "more than one GeneId/not unique" in the output indicates, that one step of the calculation (from GeneId to ElDorado Locus, to Locus in the target organism and then to GeneId in the target organism) was ambiguous, and the program does not list the GeneIds.

3. Orthologous GeneIds

For each input GeneId, the output lists the orthologous GeneIds with the corresponding gene symbol and ElDorado Locus for each selected target species. The link to the ElDorado locus will open a new window with more details on the locus (see More Gene Info page)

RegionMiner subtask: Search for orthologous GeneIds

Introduction

Parameters

Output

1. Analysis Parameters

2. Statistics of GeneIds

3. Orthologous GeneIds