ExonHunter parameters for plasmodium, packaged on 2007-02-06
To install, untar in the param directory of ExonHunter installation



Available about files:
-----------------------

est-strong.about   For ESTs of the same species as query, 
                   aligned by sim4 (or similar software)
                   
est-weak.about     For EST from a different species aligned by SIM4
                   (or similar software)

protein.about      For proteins aligned by BLASTx

repeat.about       Repeats found by repeatmasker.


Available bucket files:
-----------------------

same-est           Same species ESTs
other-est          ESTs coming from other species
other-prot         Proteins from all species
repeat             Sequence repeats


Release notes:
--------------
This version was trained using gene annotations downloaded
from plasmoDB 5.2. 

Advisors were trained using the following databases:

TIGR gene indices (now at Harvard, Dana Farber Cancer Institute):
- PBGI.release_5.zip - P. berghei - 05-17-2004    
- PFGI.release_8.zip - P. falciparum - 09-28-2004
- PVGI.release_2.zip - P. vivax - 12-09-2004     
- PYGI.release_5.zip - P. yoelii - 05-10-2004    

SWISSPROT excerpt using the following species:
- plants (ARATH, MAIZE, SOLTU, ORYSA, LYCES, WHEAT), human, C.elegans

RepeatMasker species: plasmodium

Tested on three random approx. 2MB segments of plasmodium genome
and compared to reference annotation from plasmoDB:

                              ab initio       with evidence
Transcript Sensitivity          45.06%          48.98%
Transcript Specificity          50.53%          53.09%
Exon Sensitivity                66.98%          69.63%
Exon Specificity                56.12%          58.33%
Nucleotide Sensitivity          98.60%          98.62%
Nucleotide Specificity          96.88%          96.97%


