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MHC-FIS-LdDB

MHC-I peptide Screening using Fuzzy Inference System - Leishmania donovani proteome

About

MHC-FIS-LdDB is a database of peptides (L. donovani proteome) categorized by the fuzzy inference system. The categorization is based on the six different epitope features including normalized score based on binding prediction of 27 major alleles by four different machine learning tools, normalized score from prediction of T-cell propensity, normalized score from prediction of pro-inflammatory response, normalized score form proteasome cleavage prediction, normalized score of TAP transport efficiency, and normalized score based on BLAST continuous similarity with human proteins. A total of 60 fuzzy rules were implemented to determine the probable epitope for the peptide: "Low", "Moderate", "High", or "Very High". The database has easy search capabilities and gives complete access to data. Click "Know more" for the detailed method.

How to use:

  • The database provides three search options: search by ID, search by sequence, and search by protein name. 'Search by ID' is straight forward, start typing the L.donovani protein ID (TriTryp DB Id, ex: LdBPK_010010) and select one. With a ‘protein name’ search, one can perform a text search for the protein ID of interest. Click 'ID Lookup by Protein Name' button, type the name of the protein of your interest, Copy the desired ID from ID column and paste it in "Search by ID" box in the main page. ‘Search by sequence’ performs BLAST against the L. donovani proteome and finds a protein with the highest similarity to the query protein, for which the results are automatically displayed.
  • In the ‘Explore Peptide’ section, all the parameters computed for each peptides of the protein will be listed.
  • The results can be sorted by any column.
  • The table has a search box that allows the user to search for peptides and to filter any of the categories
  • Users can expand the rows in the result table by pressing ‘+’ to view all the predicted data, including various feature scores, HLA peptide binding strength, number of identity with the human proteome, and sequence information of the protein that shares high similarity with the corresponding peptide.

Search by ID:

Example: LdBPK_010010

Search by Sequence:

Result having the highest similarity with the input sequence will be displayed! (Powered by TriTrypDB)

Search Results

No Match Found!

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Explore: No match Found!

More Info. ID Start End Peptide Population Coverage Category Score Fuzzy Output
More Info. ID Start End Peptide Population Coverage Category Score Fuzzy Output

Statistics

Total Proteins

8020

9-mers Scanned

Class Very-High

3729 (0.0772%)

Class High

6023 (0.1247%)

Class Moderate

3,36,736 (6.9%)

Class Low

Proteins not containig Very high / High category peptides

3415 (42.58%)

Fuzzy rules

60

Misc.

Contact

Dr. Saravanan Vijayakumar

Scientist, Bioinformatics/Bio-Statistics, ICMR-RMRIMS

e-mail:saravanan.vij@icmr.gov.in

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