SBC logo Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred

Fetching Q7S3C4 from www.uniprot.org...

The NucPred score for your sequence is 0.70 (see score help below)

   1  MASNSWQFAGADDESDDDNFNPAPADMSDEENNDNDEETTHNHRPAGKTV    50
  51  RQASSPVPDEEEEEEEHDEEEDARPAKRSRRDHHDDDEDEEQDEEENEEI   100
 101  DEEEEEDEEEEEDEEDEDDVHGGNRRKRRNKDRRAAFFDIEAEVDDEDEG   150
 151  EDEVGDGEEIEDFIDNAHPDDIADSGRLNDDRRHRELDRRREMEASLDAE   200
 201  KQAEILRERYGKRAPARGYGDMAIVPRRLLLPSVEDPSIWAVRCKEGKER   250
 251  EVIFSIMRRIEERMGTKNEVPITAAFERGGINSVMKGYIYVEAQRQNDIL   300
 301  VALDGILNVYPRSNMHLVEIKDMPDLLRVIKTPNLEPGAWVRLKKPAKHA   350
 351  GDLAQVIDVTENGLEARVRFIPRLDYGVRDDPVFQADGKRKRPGVPGPRP   400
 401  PQRLFSEAEARKRHPRYLQGNPQTNSWNYNGDDFENGFQVKDIKIQQLEV   450
 451  KNVNPTLEEVTKFASGAEDGTENLDLKALAATLKDSAKSVAYVPGDIIEV   500
 501  YEGEQQGVIGKATNVQGDIVTLQVTEGDLAGRTIDVPNKGLRKRFRIGDH   550
 551  VKVIGGSRFRDEVGMVVKIVDDRVTLLTDQTNTEITVFSKDLREASDIGG   600
 601  QGSLGQYSLLDLVQLDATTVGCIVKVDRESVVVLDQNGDTKQVQPSQITN   650
 651  KLPKRKFAVAADRNGSEIRLDDVVREYGGQQRQGKIIHIHRSYIFLHTTT   700
 701  TNENAGVFVTRANSVTTVAAKGGRNTATAGPDLSAMNPALKRNPTASGKQ   750
 751  MPAPRTFGPDRAINQTVVIRRGGYKGLLGIVKDTTDTHARVELHSRGKII   800
 801  TIPKADLSFKDKVTGKTIDINQRGGSRGGFGGGGRGGGEFGSRTPMASGG   850
 851  SDRTPAWGSSRSTARTPAWNRDAGGSRTPAWNDGSRTVNPYDGSRTPYGG   900
 901  ATAYGGIGSRTPAWHSGSRTPAPDSFGHGSKTPAWSAGSDSWGSKTPGYG   950
 951  ASAPTPGASGDAWGYTPGASGGGNSSSAYDAPTPGGGLSAPTPGAALNAP  1000
1001  TPGAYSAPTPAAVSAPTPGAWQGGWGSGGDAVSAPTPGALGAPTPGAPGY  1050
1051  ADDD                                                1054

Positively and negatively influencing subsequences are coloured according to the following scale:

(non-nuclear) negative ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| positive (nuclear)

with NucPred



If you find NucPred useful, please cite this paper:
NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022
The authors also look forward to your comments and suggestions.

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.)

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