Help for PredHSP ::
The submission form
To submit a protein sequence for prediction, following steps have to be followed. The numebr in parenthesis indicates the corrosponding input box of submission form (displayed in Figure 1).
- Go to submit page of PredHSP. click here to open submission page
- Enter job name/sequence name.[optional]
- Paste/upload FASTA format protein sequence.
- Select threshold of prediction.
The probability of correct prediction directly depends on the threshold. For prediction with high confidence (less probability of false positive prediction) high threshold should be choosen. At low threshold, the probability of false negative prediction is very low. On default theshold (-0.2) the rate of false negative and false positive prediction was nearly equal during training of SVM model.
- Click 'Run Prediction' to submit protein for prediction.
Figure 1: PredHSP submission page showing how to insert input sequences.
Query Sequence(s)
PredHSP process only protein sequence file in fasta format. User have option to cut and paste in the text box or directly upload the sequence file. The limits of PredHSP is upto 25 sequences at a time. If user submit more than 25 sequences, PredHSP predict only first 25 sequences. Following figure 1 is an example showing how to submit a query in PredHSP.
Example Sequence
>sp|P35193|ATG19_YEAST Autophagy-related protein 19 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=ATG19 PE=1 SV=1
MNNSKTNQQMNTSMGYPLTVYDECNKFQLIVPTLDANIMLWCIGQLSLLNDSNGCKHLFW
QPNDKSNVRILLNNYDYGHLFKYLQCQRKCSVYIGEGTLKKYNLTISTSFDNFLDLTPSE
EKESLCREDAHEDPVSPKAGSEEEISPNSTSNVVVSRECLDNFMKQLLKLEESLNKLELE
QKVTNKEPNHRISGTIDIPEDRSELVNFFTELKTVKQLEDVFQRYHDYERLSQECDSKTE
IASDHSKKETKIEVEPPNERSLQITMNQRDNSLYFQLFNNTNSVLAGNCKLKFTDAGDKP
TTQIIDMGPHEIGIKEYKEYRYFPYALDLEAGSTIEIENQYGEVIFLGKYGSSPMINLRP
PSRLSAESLQASQEPFYSFQIDTLPELDDSSIISTSISLSYDGDDNEKALTWEEL
>sp|O65719|HSP7C_ARATH Heat shock 70 kDa protein 3 OS=Arabidopsis thaliana GN=HSP70-3 PE=1 SV=1
MAGKGEGPAIGIDLGTTYSCVGVWQHDRVEIIANDQGNRTTPSYVAFTDSERLIGDAAKN
QVAMNPINTVFDAKRLIGRRFTDSSVQSDIKLWPFTLKSGPAEKPMIVVNYKGEDKEFSA
EEISSMILIKMREIAEAYLGTTIKNAVVTVPAYFNDSQRQATKDAGVIAGLNVMRIINEP
TAAAIAYGLDKKATSVGEKNVLIFDLGGGTFDVSLLTIEEGIFEVKATAGDTHLGGEDFD
NRMVNHFVQEFKRKNKKDISGNPRALRRLRTACERAKRTLSSTAQTTIEIDSLFDGIDFY
APITRARFEELNIDLFRKCMEPVEKCLRDAKMDKNSIDDVVLVGGSTRIPKVQQLLVDFF
NGKELCKSINPDEAVAYGAAVQAAILSGEGNEKVQDLLLLDVTPLSLGLETAGGVMTVLI
QRNTTIPTKKEQVFSTYSDNQPGVLIQVYEGERARTKDNNLLGKFELSGIPPAPRGVPQI
TVCFDIDANGILNVSAEDKTTGQKNKITITNDKGRLSKDEIEKMVQEAEKYKSEDEEHKK
KVDAKNALENYAYNMRNTIRDEKIGEKLAGDDKKKIEDSIEAAIEWLEANQLAECDEFED
KMKELESICNPIIAKMYQGGEAGGPAAGGMDEDVPPSAGGAGPKIEEVD
>sp|Q14568|HS902_HUMAN Heat shock protein HSP 90-alpha A2 OS=Homo sapiens GN=HSP90AA2P PE=1 SV=2
MPEETQTQDQPMEEEEVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIW
YESLTDPSKLDSGKELHINLIPNKQDQTLTIVDTGIGMTKADLINNLGTIAKSGTKAFME
ALQAGADISMIGQFGVSFYSAYLVAEKVTVITKHNDDEQYAWESSAGGSFTVRTDTGERM
GRGTKVILHLKEDQTEYLEEQRIKEIVKKHSQLIGYPITLFVEKECDKEVSDDETEEKED
KEEEKEKEEKESKDKPEIEDVGSDEEEEKKDGDKKKKKTKEKYIDQEELNKTKPIWTRNP
DDITNEEYGEFCKNLTNDWEDHLAVKHFSVEGQLEFRALLFVP
Prediction Result
In response to the submitted protein sequence(s), PredHSP generates the prediction result in tabular form. We also provide a job number, if user have any query regarding their result, he/she can contact us. Here is a sample of prediction done in response to query sequences (Figure 2).
Figure 2: Screenshot of PredHSP prediction result.
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