Edinburgh Core Database Group

Capel Group

Cohn Group

Gaido Group

Jain Group

Keast Group

Lessard Group

Little Group

McMahon Group

Mendelsohn Group

Potter Group

Southard-Smith Group

Vezina Group

Editorial Office Protocols

Automated checking protocols

Running the Probe Checker

1. Navigate to the folder which contains both the perl script ‘primer_coordinates’ and Blast applications.

sbms07689:~ eo$ cd Desktop/test/

Press enter
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2. Define the path.

sbms07689:~/Desktop/test eo$ export PATH=.:$PATH

Press enter
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3. Type ‘primer_coordinates’ followed by the input file (text windows format). 

sbms07689:~/Desktop/test eo$ primer_coordinates ArchiveXXX.txt

Press enter
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4. You will see something like the following:

Processing NM_013523.2 ...
Processing NM_007857.2 ...
Processing NM_007809.2 ...

Coordinates are stored in ArchiveXXX_processed.txt

 

This exe file was created with the evaluation version of Perl2Exe.
For more information visit http://www.indigostar.com
(The full version does not display this message with a 2 second delay.)
...
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A probe report will have been generated in the ‘test’ folder.

The filename of this report appears in the Unix shell.

(in the example above, the filename is ‘ArchiveXXX_processed.txt’)

 

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IMPORTANT - The input file should contains only 3 columns.  these are:

 

The input file must be saved as a text windows format.