CTLPred Help

  • Detailed Prediction help

    • URL Information-: The method can be accessed freely from URL http://webs.iiitd.edu.in/raghava/ctlpred.The method can be accessed through web browser like netscape,internet explorer,etc.

    Sequence Submission Form-: 

    Name of Antigenic sequence-: The name of sequence may have letters and number with the "-" or "_". All other character are non-permissible. If the name of the seqeunce is submitted with illegal characters then warning will appear ( sorry,sequence have some illegal characters). If the field is left blank, then sequence is assigned a default name "CTLPRED". The sequence name is just used for only your information. It may be a problem with ä, ö, ü for example or an empty space within the name of the sequence, which is not allowed for reasons of security. Also most of the special (i.e. non-alphabetical or non-numerical) characters are not allowed (neither in the name nor in the sequence itself).

    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 submit input from both sources or no sequence is submitted.

    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.

    Prediction Approaches-: The method has the ability to predict the CTL epitopes from the antigenic sequence on the basis of Artificial Neural Networks and Support Vector Machine.The server also allows consensus and combined prediction by using above two prediction methods.The user can only apply one prediction approaches at a single run. The consensus and combined prediction results in enhancement of specificity and senstivity respectively as comapred to indivisual approaches like ANN and SVM. The user can vary the cutoff score for all prediction approaches.

    Cut off Score-: The cut off score is used to discriminate the epitopes and non-epitopes.The user can vary the cutoff score for all prediction approaches.The peptides achieving score more then the cutoff score are predicted as epitope otherwise they are predicted as non-epitopes.if the user did not select any cutoff score then the default cutoff score of prediction methods will be used.The default cut off score at which the senstivity and specificity of prediction methods are nearly same.

    Color Display
    Overlape Display
    Tabular Display

    Color Display-:  This format dispalys all predicted CTL epitopes just by coloring the predicted epitopes.The starting residue of each predicted epitope is shown is red and while rest of the residues in blue color.The results will be dispalyed in the streches of 100 amino acids in each each line.This option is very useful in detecting CTL epitopes dense regions in the sequence.The example of Color display format is shown below.

    Overlap Display-:  This format display all ovelapping CTL epitopes in the separate lines. The display is provided with a scale which provide indication about position of the epitope in the antigenic sequence. The epitopes are shown by coloring the residues as in case of color display format.

    Tabular-:  This is the most common display format used by most prediction methods.The peptides are displayed in table in descending order of their score.The predicted CTL epitopes are shown in different background color of table. The server also provides the facility to customise the number of the top scorer peptides to be displayed in table.

    Finally click on "Submit" button.