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PADLOC-DB release v2.0.0

About

PADLOC-DB is a curated database of profile Hidden Markov Models (HMMs) and Covariance Models (CMs) for prokaryotic antiviral defence system proteins and ncRNAs, and models describing the genetic architecture of these systems. These files are used by PADLOC to locate antiviral defence systems in prokaryotic genomes. The HMMs and CMs can otherwise be used independently with HMMER, Infernal and related software.

The latest version of this database is installed when running padloc --db-update, specifc versions can be installed using padloc --db-install <version>.

What's new

This release of PADLOC-DB adds many new systems from Millman et al., 2022 (HMMs from DefenseFinder), the systems from Vassalo et al., 2022, the Juk system from Li et al., 2022, the Ddm system from Jaskólska et al., 2022, the HNH (PcaRCII) system from Birkholz et al., 2022, the MADS system from Maestri et al., 2023, several new Hma-embedded candidate systems (HECs) (Payne, unpublished), and hundreds of other phage defence candidates (PDCs) (Payne, unpublished).

The covariance models used by the PADLOC web server for retron ncRNA detection have also been included. Instructions for using these CMs with PADLOC can be found in the PADLOC repo.

Due to re-formating of the system models and metadata tables, this database is only compatible with PADLOC version 2.X.X, and not PADLOC version 1.X.X. Make sure you are using the updated version of PADLOC with this database.

What's included

padloc-db
├── hmm/                        <- Defence system protein HMMs.
├── cm/                         <- Defence system RNA CMs.
├── sys/                        <- Defence system models.
├── hmm_meta.txt                <- Metadata for HMMs.
├── cm_meta.txt                 <- Metadata for CMs.
├── sys_meta.txt                <- Metadata for system models.
├── system_info.md              <- Formatted table of system/reference information.
├── README.md                   <- Information regarding metadata fields.
├── RELEASE.md                  <- This file.
└── LICENSE                     <- Copyright information.

Release record

Release Date HMMs CMs Classifications
v2.0.0 03/08/2023 5027 21 385
v1.4.0 23/04/2022 3824 0 210
v1.3.0 14/02/2022 2974 0 181
v1.2.0 11/11/2021 2360 0 126
v1.1.0 28/09/2021 2223 0 97
v1.0.0 05/08/2021 915 0 36