ProtComp - Program for Identification of sub-cellular localization

webmaster webmaster at mail.softberry.com
Thu Oct 12 20:30:48 EST 2000


   A new program ProtComp - Program for Identification of sub-cellular localization of 
Eukaryotic proteins

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. 

	Program is installed for public use at http://www.softberry.com/pss/pss.html
    
    ProtComp:  Current, first release ProtComp includes basic scheme of localization 
prediction. Second version, which will include additional signals and characteristics of 
protein compartments, is scheduled for release by the end of the year.




Accuracy of prediction tested on known proteins from TREMBL database:
Compartment


Compartment	Number tested	% of true predictions
Nuclear		154	80.5
Plasma Membrane	80	85
Extracellular	74	58.1
Cytoplasmic	23	56.5
Mitochondrial	8	87.5
Chloroplast	17	47
Endoplasmic 
reticulum	19	63.13
Peroxisomal	6	50
Lysosomal	5	40
Golgi		11	63.16
Total:		397	63.13

Input data: Paste plain sequence to the window or upload file in Fasta format. 

Output results:
Presents scores for different networks and final conclusion in Weighted Score. 
Statistics section presents results of analysis of several sequences uploaded in 
Fasta format.

******************************************
 Seq name: Q16845,  Sequence: 
MDQNNSLPPYAQGLASPQGAMTPGIPIFSPMMPYGTGLTPQPIQNTNSLSILEEQQRQQQQQQQQQ
QQQQQQQQQQQQQQQQQQQQQQQQQQQQQAVAAAAVQQSTSQQATQGTSGQAPQLFHSQTLTTAPL
PGTTPLYPSPMTPMTPITPATPASESSGIVPQLQNIVSTVNLGCKLDLKTIALRRRNAEYNPKRFA
AVIMRIREPRTTALIFSSGKMVCTGAKSEEQSRLAARKYARVVQKLGFPAKFLDFKIQNMVGSCDV
KFPIRLEGLVLTHQQFSSYEPELFPGLIYRMIKPRIVLLIFVSGKVVLTGAKVRAEIYEAFENIYP
ILKGFRKTT

Nuclear:       Score1= 0.546 Score2= 0.690 Weighted Score= 1.236
Plasma 
membrane:      Score1= 0.306 Score2= 0.000 Weighted Score= 0.280
Extracellular: Score1= 0.360 Score2= 0.690 Weighted Score= 1.050
Cytoplasmic:   Score1= 0.369 Score2= 0.290 Weighted Score= 0.659
Mitochondrial: Score1= 0.346 Score2= 0.280 Weighted Score= 0.626
Chloroplast:   Score1= 0.350 Score2= 0.280 Weighted Score= 0.630
Endoplasmic
 reticulum:    Score1= 0.386 Score2= 0.270 Weighted Score= 0.656
Peroxisomal:   Score1= 0.380 Score2= 0.670 Weighted Score= 1.050
Lysosomal:     Score1=-0.367 Score2= 0.000 Weighted Score=-0.367
Golgi:         Score1=-0.041 Score2= 0.290 Weighted Score= 0.249

******************************************

 ________Statistic of the protein localization 
prediction___________ (%): 
Nuclear:       100.00
Plasma=  0.00
Extracellular:   0.00
Cytoplasmic:     0.00
Mitochondrial:   0.00
Chloroplast:     0.00
Endoplasmic
 reticulum:      0.00
Peroxisomal:     0.00
Lysosomal:       0.00
Golgi            0.00




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