How to Use

Query Data for Prediction
SubNucPred only requires protein sequence in FASTA format (upto maximum 25 sequences at a time). If user submit more than 25 sequences, prediction is done for first 25 sequences. Sequences can be provided either by pasting to the designated text box or can be uploaded as a text file. Following (Figure 1) is an example showing different options of data submission.

SVM Threshold
If user want prediction with high sensitivity, a low threshold should be selected. At low threshold, more prediction will be reported, but rate of false positive prediction will also be high. If user want only those predictions which are highly specific, high threshold value should be selected. At high threshold although the number of predictions will be low, but rate of false positive prediction will also be low.

Example Sequence

>sp|P07199|CENPB_HUMAN Major centromere autoantigen B OS=Homo sapiens GN=CENPB PE=1 SV=2
MGPKRRQLTFREKSRIIQEVEENPDLRKGEIARRFNIPPSTLSTILKNKRAILASERKYG
VASTCRKTNKLSPYDKLEGLLIAWFQQIRAAGLPVKGIILKEKALRIAEELGMDDFTASN
GWLDRFRRRHGVVSCSGVARARARNAAPRTPAAPASPAAVPSEGSGGSTTGWRAREEQPP
SVAEGYASQDVFSATETSLWYDFLPDQAAGLCGGDGRPRQATQRLSVLLCANADGSEKLP
PLVAGKSAKPRAGQAGLPCDYTANSKGGVTTQALAKYLKALDTRMAAESRRVLLLAGRLA
AQSLDTSGLRHVQLAFFPPGTVHPLERGVVQQVKGHYRQAMLLKAMAALEGQDPSGLQLG
LTEALHFVAAAWQAVEPSDIAACFREAGFGGGPNATITTSLKSEGEEEEEEEEEEEEEEG
EGEEEEEEGEEEEEEGGEGEELGEEEEVEEEGDVDSDEEEEEDEESSSEGLEAEDWAQGV
VEAGGSFGAYGAQEEAQCPTLHFLEGGEDSDSDSEEEDDEEEDDEDEDDDDDEEDGDEVP
VPSFGEAMAYFAMVKRYLTSFPIDDRVQSHILHLEHDLVHVTRKNHARQAGVRGLGHQS
>sp|Q15172|2A5A_HUMAN Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit alpha isoform OS=Homo sapiens GN=PPP2R5A PE=1 SV=1
MSSSSPPAGAASAAISASEKVDGFTRKSVRKAQRQKRSQGSSQFRSQGSQAELHPLPQLK
DATSNEQQELFCQKLQQCCILFDFMDSVSDLKSKEIKRATLNELVEYVSTNRGVIVESAY
SDIVKMISANIFRTLPPSDNPDFDPEEDEPTLEASWPHIQLVYEFFLRFLESPDFQPSIA
KRYIDQKFVQQLLELFDSEDPRERDFLKTVLHRIYGKFLGLRAFIRKQINNIFLRFIYET
EHFNGVAELLEILGSIINGFALPLKAEHKQFLMKVLIPMHTAKGLALFHAQLAYCVVQFL
EKDTTLTEPVIRGLLKFWPKTCSQKEVMFLGEIEEILDVIEPTQFKKIEEPLFKQISKCV
SSSHFQVAERALYFWNNEYILSLIEENIDKILPIMFASLYKISKEHWNPTIVALVYNVLK
TLMEMNGKLFDDLTSSYKAERQREKKKELEREELWKKLEELKLKKALEKQNSAYNMHSIL
SNTSAE
>sp|O74791|GRN1_SCHPO GTPase grn1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=grn1 PE=1 SV=1
MVSLKKKSKRRTTRLRSRIEKKAAESKRKQKRADKKNPQWKSRIPKDPGIPNSFPYKDKI
LAEIEEQKRIREEEKLARRASGQVDAAMEEEDAVDENGSLMISKIAEAAQASNPDDEEEF
VMEEDNLGEAPLLVDSESYEASVKADTSRKAYDKEFKKVVEASDVILYVLDARDPEGTRS
KDVERQVLASSAEEKRLIFVINKIDLVPSEVLNKWVTYLRNFFPTIPMRSASGSGNSNLK
HQSASASSTISNLLKSLKSYSAKKKLKSSLTVGVIGYPNVGKSSVINALVNRSANGRSAP
CPAGNVAGMTTSLREVKLDNKLRLVDSPGIVFPSSDSKDDLYRLVMLNAVSSTKVDDPVA
VASYILQFLSRVPGQLERMFQRYELPPLLNTSDIDTATDFLVNIARKRGRLGRGGIPNLN
AAANIVINDWHAGRIEWWAEPEVINEKNSSEVQDTQIVTEWAKEFDLNDF

Figure 1. SubNucPred submission page showing how to insert input sequences.

Prediction Result
In response to the submitted protein sequence(s), SubNucPred generates the prediction result in tabular form. In case prediction is done on the basis of unique Pfam domain, the result shows predicted location and domain based prediction in a table. If the prediction is done on the basis of SVM score, the result shows predicted location and their corresponding SVM score. Here is a sample of prediction done in response to three query proteins (Figure 2).

Figure 2. Screenshot of SubNucPred prediction result.