Citations: cite cazy_webscraper and dependencies

Cite cazy_webscraper

If you use cazy_webscraper, please cite the following publication:

Hobbs, E. E. M., Gloster, T. M., and Pritchard, L. (2022) ‘cazy_webscraper: local compilation and interrogation of comprehensive CAZyme datasets’, bioRxiv, https://doi.org/10.1101/2022.12.02.518825

This paper includes a full description of the operation and examples of use.

Hobbs, Emma E. M.; Pritchard, Leighton; Chapman, Sean; Gloster, Tracey M. (2021): cazy_webscraper Microbiology Society Annual Conference 2021 poster. FigShare. Poster. [https://doi.org/10.6084/m9.figshare.14370860.v7](https://doi.org/10.6084/m9.figshare.14370860.v7)

Cite CAZy

cazy_webscraper is entirely dependent upon the CAZy database.

Elodie Drula and others, The carbohydrate-active enzyme database: functions and literature, Nucleic Acids Research, Volume 50, Issue D1, 7 January 2022, Pages D571–D577, https://doi.org/10.1093/nar/gkab1045

Citing dependencies

cazy_webscraper depends on a number of tools. To recognise the contributions that the authors and developers have made, please also cite the following:

When making an SQLite database:

Hipp, R. D. (2020) SQLite, available: https://www.sqlite.org/index.html.

Retrieving taxonomic, genomic or sequence data from NCBI:

Cock, P.J.A., Antao, T., Chang, J.T., Chapman, B.A., Cox, C.J., Dalke, A., et al (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics, Bioinformatics, 25(11), 1422-1423.

Wheeler,D.L., Benson,D.A., Bryant,S., Canese,K., Church,D.M., Edgar,R., Federhen,S., Helmberg,W., Kenton,D., Khovayko,O. et al (2005) Database resources of the National Centre for Biotechnology Information: Update, Nucleic Acid Research, 33, D39-D45

Retrieving data from UniProt:

Cokelaer, T., Pultz, D., Harder, L. M., Serra-Musach, J., Saez-Rodriguez, J. (2013) BioServices: a common Python package to access biological Web Services programmatically, Bioinformatics, 19(24), 3241-3242.

Downloading protein structure files from RSCB PDB:

Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., et al (2022) The Protein Data Bank, Nucleic Acids Research, 28(1), 235-242.

Hamelryck, T., Manderick, B. (2003), PDB parser and structure class implemented in Python. Bioinformatics, 19 (17), 2308–2310

Retrieving and using taxonomic data from GTDB:

Parks, D.H., Chuvochina, M., Rinke, C., Mussig, A.J., Chaumeil, P., Hugenholtz, P. (2022) GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy, Nucleic Acids Research, 50(D1), D785-D794.