Decipher problem portal 12-09-2013d1607

2015-01-13

Given the reactivity of an antibody repertoire for random peptides, what were the original antigens which the antibody repertoire bound to.

-Lu's ideas for the decipher problem
--He points out that the peptides with the true epitopes are often not in the lists with the best p-value obtained from normal vs disease.  However, the peptides with the true epitopes are obtained when you look at normal vs many other diseases or a disease vs many other diseases.

-some of my notes about how decipher can be performed. . . or at least how the decipher space can be better defined (for pre 07-01-2014d1303)
--"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2014\07-01-2014d1325\Method for Decipher 07-01-2014d1345.pdf"
{
Choose peptides from 330K with t-test -> find epitopes ((Method 1 Script of Josh based on occurrence of exact match in sublibrary vs match in library) (Method 2 Use glam2 with selection of all possible 5 peptides to reduce noise)) -> Search database with epitopes ((Method 1 BLAST) (Method 2 MAST)) -> Validate findings by repeating procedure with random peptides and random life space peptides
}
---[cim_Decipher Strategy 07-01-2014d1421]
--"C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2014\05-02-2014d0954\notes on ideas for decipher.pdf" pre 07-01-2014d1303

See also
-[nmer problem portal 12-09-2013d1605]
-nice paper: [Bioinformatic requirements for protein database searching using predicted epitopes from disease-associated antibodies]

azim58wiki: