New Protcomp V 3.1 Identification of sub-cellular localization

webmaster webmaster at softberry.com
Thu Apr 5 04:28:35 EST 2001


ProtComp - Version 3.1: Program for Identification of sub-cellular localization
         of Eukaryotic proteins: Animal/Fungi  - Plants

NEW   ProtComp is available for public usage at: http://www.softberry.com/

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

   ProtComp:  Current, fifth release of ProtComp developed using
COMBINATION of database analysis of similar proteins and NEURAL NET
recognizers separately trained for Animal/Fungi and Plant proteins.
 This separation is improving the recognition accuracy, which is
   for major compartments achives  90% level. 
In this release we add predicted position of
SIGNAL peptides and TRANSMEMBRANE regions

            The program initially searches our database of proteins
with known sub-cellular location and defines the location the same as
for protein having significant similarity. If such similarity is
absent we use 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 Similar protein, different networks and the final
Conclusion:
protcompan  Thu Apr  5 01:12:03 EDT 2001
ProtComp Version 3.1. Identifying sub-cellular location (Animals&Fungi)


Seq name: sodium/hydrogen exchanger mononuclear cells of leukemia patients

Significant similarity by DBSCAN-P -  Location:Plasma membrane  S=42070
******** Signal 1-36 is found
******** Transmembrane segments are found: 128-142 160-172 190-217 286-312 390-404 
411-440 

Predicted by Neural Nets - Plasma membrane with score    7.5

Integral Prediction of protein location: Plasma membrane with score   16.0

Location weights: DBSCAN-P / Neural Nets / Integral
 Nuclear            1266.0 /        0.72 /     0.97
 Plasma membrane   42070.0 /        7.55 /    15.96
 Extracellular       620.0 /        0.92 /     1.05
 Cytoplasmic         522.0 /        0.72 /     0.83
 Mitochondrial      4740.0 /        0.71 /     1.66
 Endoplasm. retic.   540.0 /        1.47 /     1.57
 Peroxisomal           0.0 /        0.45 /     0.45
 Lysosomal             0.0 /        0.45 /     0.45
 Golgi                 0.0 /        0.54 /     0.54
  

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