ProtComp

webmaster webmaster at mail.softberry.com
Fri Oct 13 14:26:02 EST 2000


Reply about accuracy ProtComp comment:

 1) No 100% accurate approach and Psort is a good program
    You always can find example or groups of examples where
    the program is wrong
For example for Q91896 in SwissProt [SUBUNIT] HOMODIMER (BY SIMILARITY). [SUBCELLULAR LOCATION] CYTOPLASMIC

Psort Results: 47.8 %: nuclear
         21.7 %: mitochondrial
         13.0 %: cytoplasmic
          8.7 %: vesicles of secretory system
          4.3 %: cytoskeletal
          4.3 %: vacuolar
ProtComp:
Nuclear:         Score1= 0.469 Score2= 0.680 Weighted Score= 1.149
Plasma membrane: Score1= 0.252 Score2= 0.290 Weighted Score= 0.542
Extracellular:   Score1= 0.397 Score2= 0.300 Weighted Score= 0.697
Cytoplasmic:     Score1= 0.541 Score2= 0.680 Weighted Score= 1.221
Mitochondrial:   Score1= 0.273 Score2= 0.290 Weighted Score= 0.563
Chloroplast:     Score1= 0.338 Score2= 0.270 Weighted Score= 0.608
Endopl.reticulum:Score1= 0.357 Score2= 0.240 Weighted Score= 0.597
Peroxisomal:     Score1= 0.287 Score2= 0.270 Weighted Score= 0.557
Lysosomal:       Score1=-0.015 Score2= 0.000 Weighted Score=-0.015
Golgi:           Score1= 0.150 Score2= 0.000 Weighted Score= 0.150

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 _Statistic of the protein localization prediction_ (%): 
Nuclear:           0.00
Plasma membrane:   0.00
Extracellular:     0.00
Cytoplasmic:     100.00

 2) Look at the scores!, for example for nuclear Q9ZW35 even if both program wrong ProtComp (in difference with Psort) Shows that
Nuclear location practically have the same probability!

 Psort:  52.2 %: cytoplasmic
         30.4 %: mitochondrial
          8.7 %: nuclear
          4.3 %: vacuolar
          4.3 %: endoplasmic reticulum
ProtComp
protcomp  Fri Oct 13 15:25:05 EDT 2000

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 Seq name: ,  Sequence: 1MLELRLVQGSLLKKVLEAVKDLVNDANFDCSTTGFSLQAMDSSHVALVSLLLRSEGFEHYRCDRNLSMGMNLGNMSKMLKCAGNDDIITIKADDGSDTVTFMFESPTQDKIADFEMKLMDIDSEHLGIPDAEYHSIVRMPSGEFSRICKDLSSIGDTVVISVTKEGVKFSTAGDIGTANIVLRQNTTVDKPEDAIVIEMNEPVSLSFALRYMNSFTKATPLSETVTISLSSELPVVVEYKVAEMGYIRYYLAPKIEEEEDTKPE

Nuclear:         Score1= 0.392 Score2= 0.680 Weighted Score= 1.072
Plasma membrane: Score1= 0.310 Score2= 0.280 Weighted Score= 0.590
Extracellular:   Score1= 0.378 Score2= 0.340 Weighted Score= 0.718
Cytoplasmic:     Score1= 0.479 Score2= 0.670 Weighted Score= 1.149
Mitochondrial:   Score1= 0.357 Score2= 0.280 Weighted Score= 0.637
Chloroplast:     Score1= 0.379 Score2= 0.700 Weighted Score= 1.079
Endopl.reticulum:Score1= 0.365 Score2= 0.110 Weighted Score= 0.475
Peroxisomal:     Score1= 0.430 Score2= 0.330 Weighted Score= 0.760
Lysosomal:       Score1=-0.008 Score2= 0.000 Weighted Score=-0.008
Golgi:           Score1= 0.363 Score2= 0.080 Weighted Score= 0.443

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