Help



This page help the user to understand AntiInflam and how to use it effectively. Here, user can get the details of all the procedures present in the different modules in a step-wise manner. User can directly go to the particular section by clicking the respective menu present in the main table.



Peptide PredictionProtein ScanEpitope MappingSimilarity Search

Peptide Prediction



This page is designed to facilitate the user to predict antiinflammatory property of peptides. User is allowed to query by pasting one or more peptide sequences in Fasta format or upload a Fasta file as shown below. The Threshold value can be altered from -1.0 to 1.0 with 0.1 step size, to set the stringency of predictions. Click Submit button to view the result page.

Picpep-1


In the result page of Peptide prediction, query peptides are listed with scores of prediction and the predicton result(antiinflammatory or non-antiinflammatory). Results can be downloaded. User can click on a peptide for its virtual screening, a process which predict the antiinflammatory property of all of its variants.

Picpep-2



Virtual screening will create all the variants of input peptide by substituting each position of it with the all 19 other naturally occuring aminoacids. If 'n' number of aminoacids are present in the input peptide, prediction results of 'n x 19' variant peptides will be shown in tabular format.

Picpep-3

Protein Scan



This page is designed to facilitate user to scan the presence of antiinflammatory sequences in a protein. Query by pasting one or more protein sequences in Fasta format or upload a Fasta file as shown below. User can change the window length of the peptide sequences, between 5 and 30, used for prediction. The Threshold value can be altered from -1.0 to 1.0 with 0.1 step size, to set the stringency of predictions. Click Submit button to view the result page.

Picprot-1



In the result page of Protein scan, query peptides are marked with predicted epitopes(in blue colour but start with red color). User can click to view detailed result. Results can be downloaded also.

Picprot-2



In the result page of Protein scan, query peptides are listed with scores of prediction and the predicton result(antiinflammatory or non-antiinflammatory). Results can be downloaded. User can click on a peptide for its virtual screening, a process which predict the antiinflammatory property of all of its variants.

Picprot-3



Virtual screening will create all the variants of input peptide by substituting each position of it with the all 19 other naturally occuring aminoacids. If 'n' number of aminoacids are present in the input peptide, prediction results of 'n x 19' variant peptides will be shown in tabular format.

Picprot-3

Epitope Mapping



This page is designed to facilitate user to map experimentally validated antiinflammatory epitopes, into protein/peptide sequences of interest. Query by pasting one or more sequences in Fasta format or upload a Fasta file as shown below. Click Submit button to view the result page.

Picepi-1



In the result page of Epitope mapping, query sequences are aligned with experimentally validated epitopes from IEDB(Immune Epitope Databse and analysis Sourse) database. IEDB and NCBI IDs of matched epitopes are given with alignments.

Picepi-2



Following is a sample of the output file obtained after clicking on the download Results link.

Picepi-3

Similarity Search



This page is designed to facilitate user to do Similarity Search of sequence of interest, against experimantaly validated antiinflammatory Epitopes in IEDB(Immune Epitope Databse and analysis Sourse) database. User is allowed to query by pasting one or more peptide sequences in Fasta format or upload a Fasta file as shown below. Click Submit button to view the result page.

Picsimi-1



In the result page of Similarity Search, unlike exact epitope mapping, epitopes with similar sequence of query are matched. Scores for all matches are shown. Click on the link to IEDB(Immune Epitope Databse and analysis Sourse) database for viewing the details of matched epitope. Alignment of matched epitopes with the query sequences are also shown

Picsimi-3