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Stepwise HELP
Name of Protein: - This
is an optional field. It can have any alphabet and numbers with "-" or
"_".
Paste Protein Sequence: -The users can paste or type their amino acid sequence in plain format (amino acid sequence in single letter code) or in any standard format like FASTA, PIR etc.
Or Upload Sequence File :- Users can either paste their sequence in above text box or they can upload their query sequence as a text file. The sequence should be either in plain or any standard format.
Sequence format: - User should select either "Amino acids in single letter code" if sequence is in plain format, or "Standard sequence format" if sequence is in any standard format.
Prediction Approach: - The server allows the
prediction on the basis of six different approaches. One or more in combination of the six listed approaches can be used for prediction
- IgE epitope and PID
In this approach, the server will search known IgE epitopes in query protein sequence and will assign as allergen if any segment have high similarity with any known epitope. If there is a known epitope(s), then mapping of the epitope(s) is performed in the query sequence. The specificity of this approach is very high but the disadvantage is it has low sensitivity, as not all IgE epitopes of all allergens are known.
- MEME/MAST motif
In this approach, the input query protein sequence search MEME matrices created by using allergen sequences.The specificity of this approach is high with low sensitivity.
- SVM method based on amino acid composition
The SVM module is generated using amino acid composition of protein sequence of allergens and nonallergens. The threshold value used is -0.4. At this value sensitivity and specificity of this method is 88.87% and 81.86% respectively, using five fold cross-validation.
- SVM method based on dipeptide composition
The SVM module is generated using dipeptide composition of protein sequence of allergens and nonallergens. The threshold value used is -0.2. At this value sensitivity and specificity of this method is 82.78% and 85.00% respectively, using five fold cross-validation.
- Blast search on allergen representative peptides (ARPs)
In this approach, the query protein sequence search the database of 2890 allergen representative peptides (ARPs), obtained from Bjorklund et al 2005.If there is a hit, then it will assign as allergen and the ARP is shown in the result field. The accuracy of this method is very high with high sensitivity as well as specificity.
- Hybrid approach (SVMc + IgE epitope + ARPs BLAST + MAST)
In this approach, the query protein sequence is assign as allergen if any one of this mentioned method predicts it as allergen.
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