Content-type: text/html Downloads and Documentation

Welcome to the tutorial. Here, we will install the scripts and use them in a simple annotation.

To run these scripts, you may need to install these elements:

  • First, intall the required programs and modules, as explained in the downloads page.
  • Download tb.pl, bsniffer.pl, and genetuner.pl or genetuner for Win32 the same folder.
  • Download the tutorial files and extract them in the same folder. You can get these files in zip format or in tar format.
  • Go to the 'check' folder and format the template genomic sequence, called 'contig.seq'. To do that, type in the command prompt:
    formatdb -p F -i contig.seq
  • Inside the 'check' folder, create two subfolders called 'results' and 'tblastn'. This is where results and tblastn files will be stored.
  • Run tb.pl by typing at the command prompt:
    perl tb.pl
    Since no project has been provided, the project prompt will appear. Enter '1' to create a new project. Provide the paths to the required files. Remember to use '/' as folder separator, even if you are using Win32:
    • Project name: 'check'
    • Results: 'check/results'
    • Template: 'check/contig.seq'
    • Tblastn files: 'check/tblastn'
    • Protein sequences: 'check/prots'
    • Extension of protein seqs: 'aa'
    • Nucleotide sequences: 'check/seqs'
    • Extension of nucleotides: 'seq'
    The script will start performing TBLASTN comparisons, which will be stored in the 'check/tblastn' folder.
  • Run BlastSniffer:
    perl bsniffer.pl check
    This will load the 'check' project that we had created. Since no file name has been provided, the script will open the first file in alphabetical order, and will keep opening all of the files in the project until stopped. The following time BlastSniffer is called, it will keep opening files where it was stopped. After performing calculations, a combination is displayed. Inside 'check/results' there is a new folder with the name of the open protein. This folder contains a text file with 'tbn' extension which contains the TBLASTN result in a simplified format. See the BlastSniffer documentation to learn how to choose a hit combination.
  • Run GeneTuner:
    perl genetuner.pl check
    or
    perl genetuner_W32.pl check
    Since no file name was provided, GeneTuner starts opening files in the same order as BlastSniffer. See the GeneTuner documentation to learn how to define exon boundaries.