Skip to content

More visible citing information #79

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
Luxxii merged 1 commit into from
Mar 4, 2026
Merged

More visible citing information #79

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
22 changes: 22 additions & 0 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,28 @@
![de.NBI Logo](https://raw.githubusercontent.com/mpc-bioinformatics/ProtGraph/master/resources/denbi-logo-color.svg)

If you used ProtGraph please take the time to answer [our short survey](https://de.surveymonkey.com/r/denbi-service?sc=bioinfra-prot&tool=ProtGraph) to help us improve de.NBI services.


## Citing / Publication

If you use ProtGraph in your work, please cite: [https://doi.org/10.1093/bib/bbae671](https://doi.org/10.1093/bib/bbae671)

> Lux, Dominik, et al. "ProtGraph: a tool for the quick and comprehensive exploration and exploitation of the peptide search space derived from protein sequence databases using graphs." Briefings in Bioinformatics 26.1 (2025): bbae671.

```bibtex
@article{lux2025protgraph,
title={ProtGraph: a tool for the quick and comprehensive exploration and exploitation of the peptide search space derived from protein sequence databases using graphs},
author={Lux, Dominik and Marcus-Alic, Katrin and Eisenacher, Martin and Uszkoreit, Julian},
journal={Briefings in Bioinformatics},
volume={26},
number={1},
pages={bbae671},
year={2025},
publisher={Oxford University Press}
}
```


## Summary

ProtGraph in short is a python-package, which allows to convert protein-entries from the [UniProtKB](https://www.uniprot.org/) to so-called protein-graphs. We use the [SP-EMBL-Entries](https://web.expasy.org/docs/userman.html), provided by UniProtKB via `*.txt` or `*.dat`-files, and parse the available feature-information. In contrast to a FASTA-file-entry of a protein, a SP-EMBL-file-entry is
Expand Down