README.md

In richelbilderbeek/bbbq: The Bilderbeek Bianchi and Bogaart Question

bbbq

Branch || ---------|---------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------ master | | develop| |

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)

richelbilderbeek/bbbq documentation built on July 27, 2023, 2:15 a.m.