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Part of the code of Bilderbeek, Richèl JC, et al. "Transmembrane Helices Are an Over-Presented and Evolutionarily Conserved Source of Major Histocompatibility Complex Class I and II Epitopes." Frontiers in immunology 12 (2021).

Install

See install.Rmd.

Dependencies

Package	Build status
epitope-prediction	No CI
mhcnuggetsr
netmhc2pan
pureseqtmr
tmhmm

Downloads

Human proteome:

• ID: UP000005640
• Download via web browser: https://www.uniprot.org/uniprot/?query=proteome:UP000005640&format=fasta
• Direct download URL: http://richelbilderbeek.nl/UP000005640.fasta

Human proteome without selenocysteines:

• Direct download URL: http://richelbilderbeek.nl/UP000005640_no_u.fasta

Topology of human proteome:

• TMHMM topology (from human proteome without selenocysteines): http://richelbilderbeek.nl/UP000005640_no_u.tmhmm

• PureseqTM topology: https://www.richelbilderbeek.nl/UP000005640.pureseqtm [1]

References

• [1] Changed the predicted topology of TRDD1_HUMAN from [nothing] to 00 (i.e. cytosolic)