Program for Identification of sub-cellular localization of Eukaryotic proteins

[编者的话]

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