Contents

IntroductionThe server allows the prediction of potential MHC class I and MHC class II binding regions from antigenic sequences.The server can predict MHC binding regions or peptides for 97 MHC alleles.The server uses the matrix data in linear fashion for prediction.
Stepwise Help

  1. Enter the protein sequence for running prediction.The sequence can be loaded in the provided text box by cutting or pasting. The user can also upload the sequence file through browsing.Then select the format of sequence. The server accept both the formatted and unformatted sequence.The formatted sequence are accepted in almost every standard format like EMBL,PIR,etc.The server uses the ReadSeq program for reading the input sequences.

    Note: All the gaps, non standard characters except the standard protein sequence are ignored from the sequence. The sequence is accepted only in the single amino acid code.
  2. Select the MHC molecules for whome user want to run prediction.The user can select multiple MHC alleles by using the ALT or Meta Key.

  3. The user can alter the search conditions by selecting the value of the threshold.Threshold is defined as the presentage of the Top scoring peptide.for Example the one percent of the threshold will predict the one 1% of best scoring peptides from protein sequence.The lower is the value of threshold more stringent will be prediction results vice versa. For getting more detail about threshold Click Here.
  4. The server displays results in graphical as well as in text format.The user can select any of display format according his or her requirments. Each display format has a distinct useful feature.Select one display format.
    The user can limit the number of top scorer peptides to be displayed in case of tabular display format.
Result Display Formats

  • The result will be dsiplayed in following four formats.
    HTML I :This option will show the overlapping predicted MHC binders in separate lines.This is very useful for defining the boundries of overlapping binders.

    HTML II :This option will dispaly all the predicted binder in the input sequence by just coloring the residues.The N terminal of predicted binder is shown in red and all other residues in blue color.This option is very useful in detection of the promiscuous binding regions in the input sequence.The promiscious binding regions are those which bind with many MHC alleles.This optionis may helpful in locating the regions which bind with both MHC class I and MHC class II molecules.
    for example LVELAGQSLL have predicted binder for MHC molecules of both classes.This region have predicted binders for H-2Kk,HLA-DRB1*0101 and HLA-DRB1*0102.

    Graphical Profile:This is a graphical reperesentation of distribution of MHC binding propensity along the whole antigenic sequence.The peaks above the threshold line are considered as predicted binder. Any peptide having the score more than threshold score is known as Predicted binder.The X axis of the plot is showing the amino acid sequence and y axis is showing the a measure of varation in score along the sequence.
    The Graphical display also plots a graph between the threshold and predicted binders from the sequence at all the thressolds.The numberical value on the top part of Y axis is showing the maximum number of predicted binders at the minimum stringency.This display is known as the threshold profile
    .
    The server also display the results in the tabular form which is most common output from most of prediction servers. The results for each allele are represented in seprate tables.The top part of table will dispalys the name of MHC allele and the cut off score at selected threshold.The table also display the sequence of each peptide,the N terminal position of each peptide and score of each peptide.
    • TmhcPred MatricesAll the matrices for the prediction are obtained from these of servers.
    • Propred
    • MMBPred
      The server uses Addition and Multipication matrices for prediction. The addition matrices are available for-
      All MHC Class II alleles and five MHC Class I alleles HLA-A2.1, HLA-B*0702, HLA-B55,  HLA-B*5301  and    HLA-B*5401
      The multilication matrices are available for-
      All MHC Class I alleles except above mentioned five MHC class I alleles.
    TmhcPred AlgorithmThe brief description of the algorithm is provided below.The server uses two type of the matrices, Addition and multiplication matrices for prediction.

    • The overlapping peptide frames are obtained from the input antigenic sequence. Suppose the length of input sequence is x. Then n numbers of peptide frames each consisting of nine amino acids are obtained by using this formula.
      n= (x- length of each peptide frame) +1        ..I
      The following overlapping peptide frames obtained from "MERRRLWGIQS" sequence.
      MERRRLWGIQS  Sequence
      MERRRLWGI  FrameI
       ERRRLWGIQnbsp; FrameII
        RRRLWGIQSnbsp; FrameIII

  • Calculation of Score by using Addition matrices:
    1. The initial score for each peptide frame is set at 0.000.
    2. The coefficient value is assigned to each amino acid of peptide frame depending on the type of amino acid and its position in nonamer peptide from the selected matrix.The coefficient values are precalculated and stored in the tables of 20 X 9 known as quantitative matrices.The peptide score is obtained by the summation of each coefficient value.

    3. Any peptide having the score more than the selected threshold is known as predicted binder.

  • Calculation of Score by using multiplication matrices:
    1. The initial score for each peptide is set at 1.000.

    2. The coefficient value is assigned to each amino acid depending on the type of amino acid and its position in nonamer peptide from the selected matrix.

      score= initial score  *  coeffiecient value for each amino acid.
      Final score = Score * final constant
      The final constant is a also stored at the bottom of each matrix.
      Peptide score = log (Final score).
    3. The peptide having score more than logrithmic cut score at selected threshold are considered as predicted binders.





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