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 | * [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. | ||
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 | ||
Revision as of 04:10, 19 May 2014
The most difficult problem in the study of T-Cells is to figure out
- which peptides are displayed by the cell and
- 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.
Algorithms to predict which peptides are displayed:
