2. Running a program on your computer


In this exercise, we will download the source code for the gene prediction program geneid. Then, we will have a look at the routines and parameter files. Finally, we are going to repeat the process on the same sequence as in part1, but using some reannotating options to improve the accuracy of the prediction as we would do in a real situation.

Try the next steps:

  1. Connect to the GIRL web.

  2. Select Software

  3. Select geneid and then, geneid homepage

  4. Take a look around the page to answer these questions...:
    • If you have problems with the program, what can you do?
    • Imagine you would like to see any example of geneid output before testing it, you should go to...
    • You are going to download the program, what do you have to do?

  5. Let's download the program:
    • Get the geneid v 1.1. Full distribution (save the file geneid_v1.1.Jul_15_2002.tar.gz)

    • The file is compressed, try on your terminal:
      tar -zxvf geneid_v1.1.Jul_15_2002.tar.gz

    • Type cd geneid, and then make

    • Type:   bin/geneid -h

    • Take a look at the list of options

    • Save the sequence on your directory: HS307871.fa

    • Run the gene prediction:
      bin/geneid -P param/human3iso.param HS307871.fa

    • Add the option -v and try to discover how it works

    • Compare the prediction to the annotated gene

    • Reannotation from experimental results:
      From the first practice, you have observed a lack of accuracy when predicting the first exon of the gene (1107..1126), can you verify whether geneid is actually building this exon or not by running geneid to predict exons? (hint: look for the option to do it)

    • The solution for the previous step was:
      bin/geneid -xGP param/human3iso.param HS307871.fa | grep 1107

    • Let's imagine this exon has been experimentally tested and then, we'll try to rebuild the prediction with it. Take a look at this exon.

    • Reannotation process. Type and analyze the current solution:
      bin/geneid -P param/human3iso.param -R exon.gff HS307871.fa




    Josep F. Abril, Enrique Blanco, Sergi Castellano, Genis Parra and Roderic Guigó © 2002