Home |
Search |
Today's Posts |
#1
|
|||
|
|||
Protcomp 6.0 Finding sub-cellular localization of Eukaryotic proteins: Animal- Plants
Protcomp 6.0 Finding sub-cellular localization of Eukaryotic proteins: Animal-
Plants New Version 6. of Procomp is available to run at http://www.softberry.com/berry.phtml? topic=protcompan&group=programs&subgroup=proloc Softberry releases ProtComp ver. 6. The new version of popular program for prediction of protein subcellular localization, ProtComp, has overall prediction accuracy of 90% Prediction accuracy of prokaryotic version, ProtCompB ver. 2, is 95%. ProtComp combines several methods of protein localization prediction - neural networks-based prediction, direct comparison with updated base of homologous proteins of known localization; prediction of certain functional peptide sequences, such as signal peptides, signal-anchors, GPI-anchors, transit peptides of mitochondria and chloroplasts and transmembrane segments; and search for certain localization-specific motifs. The program includes separately trained recognizers for animal/fungal and plant proteins, which dramatically improves recognition accuracy. The following table provides approximate prediction accuracy for each compartment of animal and fungal proteins. Testing was performed on a sample of 1128 proteins of known localization which were NOT included in training sample for the program. Compartment Sample Size Percent predicted correctly (example for Animal) ver. 5 ver. 6 Nucleus 200 88 91 Plasma Membrane 200 87 100 Extracellular 200 83 86 Cytoplasm 199 63 88 Mitochondria 129 82 89 Endoplasmic Reticulum 107 83 82 Peroxisome 34 97 91 Lysosome 12 91 100 Golgi 47 77 91 Output sample: ProtComp Version 6. Identifying sub-cellular location (Animals&Fungi) Seq name: QUERY, Length=376 Significant similarity in Location DB - Location:Cytoplasmic Database sequence: AC=P08319 Location:Cytoplasmic DE Alcohol dehydrogenase class II pi chain precurs Score=14845, Sequence length=391, Alignment length=365 Predicted by Neural Nets - Extracellular (Secreted) with score 2.4 Integral Prediction of protein location: Cytoplasmic with score 14.7 Location weights: LocDB / PotLocDB / Neural Nets / Tetramers / Integral Nuclear 0.0 / 0.0 / 0.71 / 0.00 / 0.71 Plasma membrane 0.0 / 0.0 / 0.73 / 0.00 / 0.73 Extracellular 0.0 / 0.0 / 2.42 / 0.00 / 2.42 Cytoplasmic 14845.0 / 18465.0 / 0.83 / 8.50 / 14.68 Mitochondrial 0.0 / 0.0 / 0.70 / 0.00 / 0.70 Endoplasm. retic. 0.0 / 0.0 / 0.70 / 0.50 / 1.21 Peroxisomal 0.0 / 0.0 / 0.49 / 0.00 / 0.49 Lysosomal 0.0 / 0.0 / 0.33 / 0.00 / 0.33 Golgi 0.0 / 0.0 / 0.40 / 0.00 / 0.40 LocDB are scores based on query protein's homologies with proteins of known localization. PotLocDB are scores based on homologies with proteins which locations are not experimentally known but are assumed based on strong theoretical evidence. Neural Nets are scores have been assigned by neural networks. Tetramers are scores based on comparisons of tetramer distributions calculated for QUERY and DB sequences. Integral are final scores as combinations of previous four scores. While interpreting output results, it must be kept in mind that: 1. ProtComp's scores per se, being weights of complex neural networks, do not represent probabilities of protein's location in a particular compartment. 2. Significant homology with protein of known location is a very strong indicator of query protein's location. 3. For neural networks scores, their relative values for different compartments are more important than absolute values, i.e. if the second best score is much lower than the best one, prediction is more reliable, regardless of absolute values. 4. If both neural networks and homology predictions point to the same compartment, this is very reliable prediction. --- |
Reply |
Thread Tools | Search this Thread |
Display Modes | |
|
|