MHC2Pred:SVM based method for MHC class II binders prediction

MHC2Pred Help

The MHC2Pred is an SVM based method for prediction of promiscuous MHC class II binding peptides.The average accuracy of SVM based method for 42 alleles is ~80%. The performence of the method was poorer for few allele due to smaller size of dataset. The performence of the method was tested through 5-fold cross-validation. The data for training has been extracted from MHCBN and JenPep database.This method will be useful in cellular immunology, Vaccine design, immunodiagnostics, immunotherapeuatics and molecular understanding of autoimmune susceptibility. The stepwise help for using the server and snapshot of submission page with approriate labelling has been described below:-

Antigenic sequence-: This server allows the submission of sequence in any of the standard formats. The user can paste plain sequence in the provided text area.The server also has the facility for uploading the local sequence files. Amino acid sequences must be entered in the one-letter code.All the non standard characters like [*&^%$@#!()_+~=;'",<>?.\|} are ignored from the sequence.The minimum length of the submitted sequence should be nine otherwise server will show warning message.The warning is also displayed if the user submitted sequences from both sources.

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Format of Antigenic sequence-: The server can accept both the formatted or unformatted raw antigenic sequences.The server uses ReadSeq routine to parse the input.The user should choose wether the sequence uploaded or pasted is plain or formatted before running prediction.The results of the prediction will be wrong if the format choosen is wrong.

Selection of Allele-: The user can vary the number of the Allelles before running prediction.The server allows the selection of multiple alleles through Alt or Meta key.The selection of the multiple alleles is crucial for prediction of promiscious MHC binders or T cell epitopes. The error message displayed in case no MHC allele is selected.

Threshold-: The threshold is used to discriminate the MHC binders from non-binders..The user can vary the threshold score between -1.5 to 1.5.The peptides achieving score more then the cutoff score are predicted as binders otherwise they are predicted as non-binders.if the user did not select any cutoff score then the default threshold of prediction methods will be used.The default threshold is that at which the senstivity and specificity of prediction methods are nearly same.

Prediction Results-: The results of the prediction displayed in user-freindly text formats.Each of result display format firstly provides a compehensive account of length of input sequence,prediction approach,nonamers generated and threshold as shown below.

MHC2Pred Help

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