Kinannote Files

To set up and run Kinannote:

1. Unpack the tarball (tar -xvf Kinannote_1.0.tar) in the directory in which you want Kinannote to live.
   The name of the unpacked directory will be "Kinannote_1.0".

2. cd into the Kinannote_1.0 directory. There is a script here that will
   take paths to HMMER2 and BLAST installations that have 'hmmsearch'
   and 'blastall' entered by the user, and get them into the right
   place in Kinannote so that it will run.

   The setup script will also check that Kinannote has the libraries
   and modules it needs to run, and, for the user's convenience,
   take a stab at finding appropriate HMMER and BLAST installations.
  
   To run the setup script enter
   
   perl setup_kinannote.pl

   Follow the instructions in the script, and a file named 
   "Kinannote_1.0.pl" will appear in the Kinannote_1.0 directory.
   This is a working version of Kinannote.

3. cd into the Kinannote_1.0/test directory. This directory contains "spombe.fasta"
   an S.pombe proteome fasta file to test Kinannote. Enter this command to
   run Kinannote:

   perl ../Kinannote_1.0.pl -c Spom spombe.fasta

   Appearance of the following lines in standard output confirms the installation:

Done!

The number of uniquely-identified sequences in spombe.fasta is 5142
The number of ePKs in spombe.fasta is 109: ePKs comprise 2.120 % of this proteome
The fraction of core ePK families found in this proteome is 0.938 (1 is best)
A list of hits with standardized names may be found in spombe.names
A summary of this kinannote run may be found in spombe.run_summary

ALERT! By default Kinannote assumes input is non-metazoan, so that
it does not inappropriately "discover" TK group kinases outside of the metzoans.
Potential TKs are flagged in the draft_kinome table but classified TKL.

TO CLASSIFY TKs IN METAZOANS RUN KINANNOTE WITH THE '-m' OPTION!

   perl ../Kinannote_1.0.pl -m -c Meta metazoan.fasta

For more details see ./doc/Kinannote_1.0_documentation.pdf