 | Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden. |
NucPred
Fetching Q4WK35 from www.uniprot.org...
The NucPred score for your sequence is 0.95 (see score help below)
1 MSSTAQKNSLSPTGNGVTKRKSGSAACVHCHRRKVRCDARIVGLPCSNCR 50
51 SSGKTDCRIHEKKKRLAVRSILNPVPIRCRPPSTSEHVPEASPPSTISEP 100
101 TAFTTAFRGVQPEAAAPPASVAPNVQSKAQHLHSNSYSQTSPQAQECHLP 150
151 PASDRFAEQDAHADFEKRLVKLIDDEEGSGPREIQRGVRAIYVGHELSNM 200
201 SFLIRQQRDKDDDVYHFAGSEIPRRQLKTGHDQLLVDALTLPEPALVDEL 250
251 VQAYFTHVNPGYPIVEEDQFMSQYRNRDPSDPPPILLLQAILLVGCHVTH 300
301 PKEERDALKAIFFRRAKWLFDNRIERNRDTLVQAALLLTWHSDSPDDDVS 350
351 ANAHYWVGVAARIATGLGMHRNPVSSRFAPRDRRMWRRLWYILVQLDVMV 400
401 SLSYGRPQAINLEDSDVSPLTASDFEGCGARVQTDYVIHFSELCTMISYI 450
451 VRERFGLRVSSERRKAALQEADEALANWSLRLPDHLRLRASDMDPWSAML 500
501 HLTYNNFLILLHRPHPRASAYSDDYGPHDAEICSAAAGVITSIFEELRLN 550
551 DRLKYLWYSGVHTLFTAMIQVRVELRFSNPVLAINALRRFDSASCSLREL 600
601 AKYWSHATTILRLFEDSKRLQKDLRLATSERSRPFSSTQDQPQAQALDQN 650
651 KNQHQHSSADAPVQPPQPDRLLPSYDSPTPDSTSLPQTAVSPHQNLTFDS 700
701 WIPSTNLATVDPMDQPREFLDWRQLFSFTDPDQPVLPMSMDGLPELEDEW 750
751 RQIYWQETPMSDLLQDGGWMHG 772
Positively and negatively influencing subsequences are coloured according to the following scale:
(non-nuclear) negative ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| positive (nuclear)
What does the NucPred score mean?
You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper. |
NucPred score threshold | Specificity | Sensitivity |
see above | fraction of proteins predicted to be nuclear that actually are nuclear | fraction of true nuclear proteins that are predicted (coverage) |
0.10 | 0.45 | 0.88 |
0.20 | 0.52 | 0.83 |
0.30 | 0.57 | 0.77 |
0.40 | 0.63 | 0.69 |
0.50 | 0.70 | 0.62 |
0.60 | 0.71 | 0.53 |
0.70 | 0.81 | 0.44 |
0.80 | 0.84 | 0.32 |
0.90 | 0.88 | 0.21 |
1.00 | 1.00 | 0.02 |
Sequences which score >= 0.8 with NucPred and which
are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.) |
Go back to the NucPred Home Page.