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You can download the latest version from http://hordeum.oscs.montana.edu/genographer
There was a bug in the original program that caused it to have problems with these files. It has been fixed as of January 8, 1999. Download a newer version if you have not done so already.
You can import lanes from any gel into Genographer. However, the intensity of the lanes in different gels often varies. One can now normalize a gel within Genographer. Go to the "Gel" menu and select either "Normalize on Total Signal" or "Normalize on Partial Signal."
See the previous questions.
Make sure you are using GeneScan 2.1. Genescan 2.01 does not seem to work. (Legal Note: GeneScan is a registered trademark of Perkin-Elmer).
If this doesn't work see, see this question.
Genographer only works with lanes from the ABI 37x at this time. I have no plans to add support for scanned images, but perhaps someone else will. It would certainly be a good thing. From a scanned image, the following information is needed by Genographer:
In short, no. It's written in Java, so it should run in most places. It may not be perfect, but it should work. If somebody else would like to port it, go for it.
Most likely, the program is running out of memory. See the "Memory" section in the help file.
To be honest, I don't know. It only appears on some systems and has something to do with the way graphics are handled. I don't know a lot about that area, so I'm not planning on trying to fix the problem. On occasion, the screen will not be redrawn properly. Either hit the "Gel" button again, scroll some more, or select "Gel|Redraw Gel" from the menu.
Look at the files in the Genographer directory. There is a good chance they look like "genogra.cla" Some older unzip programs don't understand long filenames and revert to the 8.3 format used by DOS. However, Java needs the long filenames. Try using a different program to unzip the files. They should have long names, like "genographer.class"
This is a bug. The first time one double clicks on the parent directory "../" nothing happens. Double clicking a second time works. This only occurs the first time one clicks on the "../" after the dialog box is opened. For all of the times after that, it works properly.
Usually this occurs when Genographer cannot find the file. First, make sure the file is in the same directory has the file genographer.class. If you are running it from a Win95/98 shortcut, make sure that the "Start In" option is set to the path that contains genographer. If you are starting from the command prompt, make sure you start in the directory that contains genographer. On the Mac, the notion of a start in directory does not exist as far as I can tell. In this case, you can pass the directory that Genographer should start in as a command line parameter. You may want to look at the JBindery tool for the Mac. For example, the command line would become:
jre -cp c:\genographer genographer c:\genographerFor the make, use the JBindary to set the class path and then add the path in the "Optional Parameters" section of the command screen. It will look something like "Macintosh HD/Genographer", but I am not sure of this. It hasn't been test. If someone finds the correct solution, please let me know.
You can also use the optional command line preference to make the program easier to start in Unix.
This information is sent to the standard output of the system. If you run the command jrew it will not start a DOS window with Java and the standard output will not appear. Use jre to see this information. Of course, the previous only applies to Windows machines. On Unix machines, it depends on where the standard out is going. Usually it goes to the window that started the program, unless you fork it off, in which case it may not appear. If you use a button of some sort to start it, it probably won't appear at all. On the Mac, use JBindery to set the Standard Output redirection.
See the above question. This is printed to standard out.
The problem comes from the way Motif handles display clipping. It's somewhat different then Win95, and is quite annoying. To fix the problem, all of the sizes of the components must be changed. These are all easily accessible values in the source files. Let me know if you want help fixing the problem.
This problem occurs when a size standard is missed. Some times, GeneScan misses the 50bp size standard. The best way to correct this problem in my experience is to lower the minimum intensity required to detect a peak in the size standard and then reanalyize the sample in GeneScan. Make sure you use the current Analysis Parameters when you do.
The problem results from the way Genographer sizes the lanes. See the section in the help files on Sizing. Follow the Program Features link. The reason in the case of the "Local Southern" method is that the program assumes the start of the lane is 0bp and that the scale is linear from that point until the first size standard. However, this does not seem to be a very good assumption. I would not recommend trying to analyze the data until you can convince GeneScan to pick up the 50bp. Luckily, this problem will not affect the sizing of most of the rest of the gel.
Genographer used to export a PPM image format, which is not very wide spread. Genographer now (1/8/99) exports a PNG image, which should be read by many programs. It is a newer format, so some old programs do not support it, but most newer ones should. The latest versions of both Microsoft PowerPoint and Corel Presentations handle PNG graphics.
First, make sure you've checked the help files. If that doesn't work, feel free to contact me. I'd like to here suggestions as well.
I can be reached at: james_benham@hmc.edu
If that doesn't work, you can also try Tom Blake at blake@hordeum.oscs.montana.edu
Thanks for your interest.
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