News
The entire operating system has been updated to the new OS 22.04 Ubuntu, and Python modules have been updated to the latest versions. As a result, seed differences may occur.
Please inform us if you encounter any issues or unexpected results. Also, If you encounter any bugs or issues during your job, please feel free to contact us via email (16/Feb/2024).
1. PGPT Ontology, Download section for PGPT-Pred/mgPGPT data and Krona Download option available
a) You are interested in genes related to specific PGP functions? Then you use the PGPT Ontology page. Here, you can look up functions, genes or KEGG K numbers.
b) Further, we provide the PGPT protein fasta and for metagenomics the mgPGPT protein fasta and MEGAN mapping files. Detailed information is given at the Download page.
c) We also provide a result download option of the hierarchical classifiaction as presented in the respective KRONA plot.
About Us
In collaboration between the University of Tübingen (Algorithms in Bioinformatics), the Leibniz Institute of Vegetable and Ornamental Crops - IGZ Grossbeeren (Beneficial plant-microbe interactions), the Julius Kühn Institute - Federal Research Center for Cultivated Plants (Institute for National and International Plant Health) and the Centre for Plant Biotechnology and Genomics – CBGP Madrid (Phytopathogenic Bacteria) we are continuously establishing novel methods and resources to classify plant-associated microbes among others.
The joint work, is mostly promoted by Sascha Patz (UT), Anupam Gautam (UT & IMPRS-"From Molecules to Organisms", Max Planck Institute for Biology Tübingen), Silke Ruppel (IGZ), Matthias Becker (JKI), Pablo Rodríguez Palenzuela (CBGP), and Daniel H. Huson (UT) and constitutes an initiative to collect current knowledge about plant-associated microbes in one comprehensive web platform. We encourage all researcher around the world to contact us and to share your ideas on how to improve or extend our services.
1. Patz S, Rauh M, Gautam A, Huson DH. mgPGPT: Metagenomic analysis of plant growth-promoting traits. (to be submitted, meanwhile you can read the preprint
2. Patz S, Gautam A, Becker M, Ruppel S, Rodríguez-Palenzuela P, Huson DH. PLaBAse: A comprehensive web resource for analyzing the plant growth-promoting potential of plant-associated bacteria. (to be submitted, meanwhile you can read the preprint)
3. Becker Y, Patz S, Werner S, Hoppe B, Feltgen S, Berger B, Schikora A, Glenz R, König S, Erler S, Schrader G, Huson DH, Becker M. Bacteria producing contractile phage tail-like particles (CPTPs) are promising alternatives to conventional chemical pesticides. Journal of Cultivated Plants. 2022 (LINK)
4. Martínez-García PM, López-Solanilla E, Ramos C, Rodríguez-Palenzuela P. Prediction of bacterial associations with plants using a supervised machine-learning approach. Environ Microbiol. 2016 (LINK)
5. Patz S, Becker Y, Richert-Pöggeler KR, Berger B, Ruppel S, Huson DH, Becker M. Phage tail-like particles are versatile bacterial nanomachines – A mini-review. Journal of Advanced Research. 2019 (LINK)
6. Ashrafi S, Kuzmanovic N, Patz S, Lohwasser U, Bunk B, Spröer C, Lorenz M, Frühling A, Neumann-Schaal M, Verbarg S, Becker M, Thünen T. Two new Rhizobiales species isolated from root nodules of common sainfoin (Onobrychis viciifolia) show different plant colonization strategies. Microbiol Spectr. 2022 (LINK)
7.Patz S, Gautam A, Becker M, Schrader G, Huson DH. CPTPdb/-Pred: A database and prediction tool for bacterial R-type tailocins and their antagonizing potential against pathogens. (in preparation)
PLEASE CITE THE RESPECTIVE REFERENCES WHEN PUBLISHING ANY RESULT CURATED VIA OUR SERVICES. SEE REFERENCE NUMBERS BELOW EACH SERVICE. THANK YOU!
Services
PLaBA-db
Screening for approx. 5,565 plant-assciated bacteria, their plant isolation site, plant interaction phenotype and PGPT annotations, among others.
(CITE REFERENCE 1,2)
PIFAR-Pred
Annotation of plant bacterial only interaction factors (proteins) “PIFAR” leads to determination of a plant-associated bacteria, using blastp+hmmer against the PIFAR protein collection and classification.
Upload restricted to 8,000 proteins.
(CITE REFERENCES 1,2,4)
PGPT-Pred
Annotation of bacterial plant growth-promoting traits (proteins) "PGPTs" using blast (relaxed mode) and blastp+hmmer (strict) or IMG-KEGG-annoation mapping against the PGPT ontology.
Upload restricted to 8,000 proteins.
(CITE REFERENCES 1,2,6)
CPTP-db
Screening for potential tailocin encoding bacteria in public datasets and their putative target bacteria based on protein homology.
(CITE REFERENCES 1,2,3,5,7)
[Access restricted!]
CPTP-Pred
Annotation of potential tailocin syntenic gene clusters and their putative target bacteria based on protein homology, synteny and HMM-Models.
(CITE REFERENCES 1,2,3,5,7)
[Access restricted!]
Version History and Warranty
PLaBAse v.1.02 - Mar 2022
Copyright (C) 2020-2024 Sascha Patz. This web platform and all its services/tools come with ABSOLUTELY NO WARRANTY.
All services (if not restricted) are freely available for ACADEMIC NON-profit institutions, otherwise do not hesitate to contact us by email at plabase[at]inf.uni-tuebingen.de.
