Starting with Genefinder

Genefinder is available in two forms, a text based program genefinder and one with a graphical display xgenefinder. Both should be in your search path, as they are located in the directory /usr/local/bin. The difficult part with genefinder is using the organism specific tables that help define gene positions. The distribution comes with four, and we have an additional Arabidopsis set from the European Sequencing group. The table name files are located in the directory /usr/local/lib/genefinder and are named as follows If you have a DNA sequence in fasta format with the name "mysequence.seq" and you wish to run xgenefinder with the nematode tables, you may run with a command similar to the following;

xgenefinder -tablenamefile /usr/local/lib/genefinder/nemtables mysequence.seq

You need to include the full path to the table name file, therefore if you always want to run using a particular set of tables, you can save yourself some typing by creating a file call .genefinderrc in your home directory with the line:

tablenamefile: /usr/local/lib/genefinder/nemtables

Addional notes on setting parameters and the .genefinderrc file are available in the file Humangenefinding.html The main documentation file is genefinder.doc.