Genefinderdocumentation
Humangenefinding
Makingtables

On the SAF the following tables are available:

  /usr/local/share/genefinder/drostables
  /usr/local/share/genefinder/humtables
  /usr/local/share/genefinder/thaltables
  /usr/local/share/genefinder/nemtables
  /usr/local/share/genefinder/wormtables
  
The last two are identical and are the default.  To see
the available command line options issue this command:

 % genefinder -help
 
It is best to run genefinder from within sh or bash like this:

 % bash   change to the bash shell
 % genefinder -tablenamefile /usr/local/share/genefinder/humtables \
     myseq.nfa >gf_stdout.txt 2>gf_stderr.txt

which will produce the follwing files:

gf_stderr.txt               Error messages (normally empty)
gf_stdout.txt               Output messages (details of results)
temp.all.scorepairs         temporary file, can be deleted
temp.gene.scorepairs        temporary file, gives regions and scores
translated.predicted.genes  Predicted genes, translated and exons assembled

The accessory programs tables and so forth
are kept in the directory:

 /export/home/allprogs/gf/genefinder/bin