DOWNLOADS !!! Currently under development !!!

If you are using the file below, please cite the references (1,2) listed below.

1. Patz S, Rauh M, Gautam A, Huson DH. mgPGPT: Metagenomic analysis of plant growth-promoting traits. (submitted 2024, 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. (submitted 2021, meanwhile you can read the preprint)

If you are utilizing an AnnoTree-enhanced file, kindly cite the following reference as well.

3. Gautam A, Felderhoff H, Bağci C, Huson DH. Using AnnoTree to get more assignments, faster, in DIAMOND+ MEGAN microbiome analysis . Msystems. 2022 Feb 22;7(1):e01408-21.(Link)
4. Mendler K, Chen H, Parks DH, Lobb B, Hug LA, Doxey AC. AnnoTree: visualization and exploration of a functionally annotated microbial tree of life. Nucleic acids research . 2019 May 21;47(9):4442-8.(Link)

For DIAMOND+MEGAN6 use please cite:

5. Gautam A, Zeng W, Huson DH. DIAMOND+ MEGAN Microbiome Analysis. In Metagenomic Data Analysis 2023 Jun 3 (pp. 107-131). New York, NY: Springer US.(Link)
6. Huson DH, Beier S, Flade I, Górska A, El-Hadidi M, Mitra S, Ruscheweyh HJ, Tappu R. MEGAN community edition-interactive exploration and analysis of large-scale microbiome sequencing data. PLoS computational biology . 2016 Jun 21;12(6):e1004957.(Link)
7. Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nature methods . 2015 Jan;12(1):59-60.(Link)

PLaBAse Genome Analysis Downloads (used in PGPT-Pred, PLaBA-db)

S.No	Type	Description	Statistics	Date	Download
1.	PGPT-db (fasta)	PGPT related protein reference sequences for e.g., BLASTp database	Total: 6,965,955 sequences	01/08/2021

Metagenome Analysis Downloads (e.g., DIAMOND+MEGAN6/-LR)

The current MEGAN version 6.23.4 comes along with the PGPT viewer for visualisation of metagenomic read-to-PGPT mappings of short or long reads, achieved via the DIAMOND+MEGAN pipeline.
Applicable options:

1) If your interest is only in describing PGPTs and their taxonomic affiliations, you can go with the below provided files for I) generating the DIAMOND alignment protein database using mgPGPT protein reference sequence fasta file (below #1.A mgPGPT-db) and II) mapping the aligned reads against the mgPGPT mapping database (below #1.B mgPGPT-mapping-db) with the daa-meganizer or MEGAN GUI MEGANIZATION.
2/3) If you aim at describing taxonomic, entire functional (KEGG, SEED, ...) and PGPT contents, you might either align and map your reads against the NCBInr protein reference sequences and NCBInr-mgPGPT mapping database, both provided soon, or against the AnnoTree protein reference sequences (here) and AnnoTree-mgPGPT mapping database (below #2. AnnoTree-mgPGPT-mapping-db). RECOMMENDATION: For entire description of environmental samples we recommend using the AnnoTree-MEGAN approach.

The results are visible in MEGAN PGPT viewer, that shows the entire PGPT ontology and assigned reads.

S.No	Type	Description	Statistics	Date
1.A	mgPGPT-db (fasta)	mgPGPT related protein reference sequences for e.g., DIAMOND database. Enriched by proteins from AnnoTree e.g., from MAGs	Total: 39,582,183 sequences	01/02/2022
1.B	mgPGPT-mapping-db (megan)	mgPGPT-mapping database when using mgPGPT-db (#1.A) instead of NCBInr- or AnnoTree-based analysis. Unzip before use!		01/02/2022
2.	AnnoTree-mgPGPT-mapping-db (megan)	AnnoTree mgPGPT-mapping database when using instead of NCBInr- or mgPGPT-based analysis. Unzip before use!		01/03/2022

PLaBAse History

(Here, we provide a history that lists any changes or added terms regarding PGPTs, CPTPs, ... with time mark, and announce new Service versions.)

S.No	Type	Description	Statistics	Date	Download
1.	PGPT-log (Excel file, .xlsx)	PGPT ontology log file		10/08/2021