ProtComp V4, sub-cellular localization, incorporates recognition of GPI-anchor sites

webmaster_softberry_com at acedsl.com webmaster_softberry_com at acedsl.com
Thu Dec 13 08:17:59 EST 2001


ProtComp - Version 4: Program for Identification of sub-cellular localization 
of Eukaryotic proteins: Animal/Fungi - Plants

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New release of our program for predicting protein sub-cellular localization, 

ProtComp http://www.softberry.com/protein.html

 incorporates recognition of GPI-anchor sites and some other improvements. 

The third release of ProtComp includes separately trained recognizers for 
animal/fungal 
and plant proteins. Such separation dramatically improves recognition accuracy, 
which 
for major compartments, such as plasma membrane, nuclear, extracellular, 
achieves 70-90% level. 

The program is based on complex neural-network recognizers, which identify 
probability 
of the subcellular localization in nucleus, plasma membrane, extracellular, 
cytoplasmic, 
mitochondrial, chloroplast, endoplasmic reticulum, peroxisomal, lysosomal or 
Golgi compartments. 
Example of Output results: Presents scores for different networks and the final 
conclusion. 

Output sample:

Protcomp Version 4. Identifying sub-cellular location (Animals&Fungi)

Seq name: P52307 552 580
Significant similarity in Location DB -  Location:Plasma membrane  S=9390, 
LS=576 LA=450
Predicted by Neural Nets - Plasma membrane with score    2.3
******** Potential GPI-anchor in position 552 is found
Integral Prediction of protein location: Plasma membrane with score    4.3
Location weights:     LocDB / PotLocDB / Neural Nets / Integral
 Nuclear                0.0 /      0.0 /        0.73 /     0.73
 Plasma membrane     9390.0 /      0.0 /        2.26 /     4.34
 Extracellular       6200.0 /      0.0 /        1.95 /     3.33
 Cytoplasmic            0.0 /      0.0 /        0.72 /     0.72
 Mitochondrial          0.0 /      0.0 /        0.74 /     0.74
 Endoplasm. retic.      0.0 /      0.0 /        0.62 /     0.62
 Peroxisomal            0.0 /      0.0 /        1.14 /     1.14
 Lysosomal              0.0 /      0.0 /        0.28 /     0.28
 Golgi                  0.0 /      0.0 /        0.28 /     0.28


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