CgiHunter FAQs

If you have a question that is not covered by our FAQs, feel free to contact us (CgiHunter@mpi-inf.mpg.de).

Question: I have downloaded CgiHunterLight and unpacked the archive, what next?

Answer: Open a commandline shell, change into the CgiHunterLight directory and enter depending on your operating system python CgiHunterLight.py -x TestRun.xml or CgiHunterLight.py -x TestRun.xml
The CgiHunter software will then compute CpG island annotations for the human chromosome 21 and 22. The output will be placed in the subfolder Results.

Question: The TestRun was successful. How can I now compute annotations for different sequences and parameters?

Answer: Open the XML-file TestRun.xml with your favorite editor and change the configurations. For the annotation of different sequences you need to specify new tags. To change the thresholds for the CGI annotation, you can change the parameters minLength, gcContent and ratioObsExp. Save the file under a new name and restart the computation.

Question: I have no experience with python, can I use CgiHunter anyway ?

Answer: Yes. Simply install Python 2.4 on your computer (obtainable from Download Python 2.4).

Question: Will CgiHunter also run with other versions of Python ?

Answer: Yes, but it may require a few adaptations. In many cases it will be easier to install Python 2.4 instead of making these adaptations. If this is not possible feel free to contact us.

Question: Why is program called CgiHunterLight ?

Answer: CgiHunter was developed as software for the high-throughput annotation of all available vertebrate genomes. Furthermore, for each genome several parameter configurations need to be tested.
To optimize this process the software provides a large number of tuning parameters that purely influence the runtime. To study the algorithmical implications of CGI definitions, the software also provides options to identify and output every region that meets the defined parameters although most of these regions overlap each other. If these options are accidentally activated this leads to high I/O and produces large amounts of mainly redundant data.
To ensure that new users can quickly start using the software without running into these problems, we created a light version of CgiHunter. It has less tuning parameters and produces CGI Shadow annotations per default. If you are interested in becoming an expert user, feel free to contact us or make use of the provided documentations.

Question: Is there an easier way to generate the XML files?

Answer: Yes, you can start the Graphical user interface CgiHunterGUI.py. You can interactively click your way trough the dialogs and in the end store the resulting XML file. The interface was disigned for the expert version and contains a number of parameters that are only relevant if you want to generate Cgi annotations for a large number of genomes and parameters. A more detailed explaination of the interface can be found in the folder doc in the document Expert_CgiHunter_User_Manuel.pdf

Question: My question is neither covered by the FAQ nor the documentation. What can I do ?

Answer: Questions can only enter the FAQ if they are frequently asked and the documentations only highlight the main features of the program. So help us to improve the situation by sending us your questions!