T-cell epitope databases and algorithms: Difference between revisions

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Databases of peptides:
Databases of peptides:
* [http://srs.bioinformatics.nl/hspv/ HSPV]: Big list of peptides derived from RefSeq and dbSNP, not annotated at all
* [http://srs.bioinformatics.nl/hspv/ HSPV]: Big list of peptides derived from RefSeq and dbSNP, not annotated at all. Downloadable as a fasta file.
* [http://ludwig-sun5.unil.ch/CancerImmunomeDB/ Ludwig CancerImmunomeDB]: database of cDNA clones, some which annotated to react to serum
* [http://ludwig-sun5.unil.ch/CancerImmunomeDB/ Ludwig CancerImmunomeDB]: database of cDNA clones and cancer type, some are annotated to react to serum. Not downloadable.
*  
* [http://cancerimmunity.org/peptide/ Cancer Immunity Peptide list]: curated from papers, annotated with cancer, HLA and paper. Easy to scrape.
* [http://cvc.dfci.harvard.edu/tadb/ TADB]: Not online anymore?


Algorithms to predict which peptides are displayed:  
Algorithms to predict which peptides are displayed:  
* [http://www.syfpeithi.de/bin/MHCServer.dll/EpitopePrediction.htm SYFPEITHI] - proprietory
* [http://www.syfpeithi.de/bin/MHCServer.dll/EpitopePrediction.htm SYFPEITHI] - proprietory
* [http://www.cbs.dtu.dk/services/NetMHC/ NetMHC] - downloadable
* [http://www.cbs.dtu.dk/services/NetMHC/ NetMHC] - downloadable

Latest revision as of 09:05, 19 May 2014

The most difficult problem in the study of T-Cells is to figure out

  1. which peptides are displayed by the cell and
  2. which T-Cell receptor binds to which peptide

Databases of peptides:

  • HSPV: Big list of peptides derived from RefSeq and dbSNP, not annotated at all. Downloadable as a fasta file.
  • Ludwig CancerImmunomeDB: database of cDNA clones and cancer type, some are annotated to react to serum. Not downloadable.
  • Cancer Immunity Peptide list: curated from papers, annotated with cancer, HLA and paper. Easy to scrape.
  • TADB: Not online anymore?

Algorithms to predict which peptides are displayed: