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Releases: padlocbio/padloc-db

v2.0.0

17 Oct 02:15
@leightonpayne leightonpayne
v2.0.0
7f99b47
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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et al., 2022, the MADS system from Maestri et al., 2023, several new Hma-embedded candidate systems (HECs) (Payne, unpublished), and hundreds of other phage defence candidates (PDCs) (Payne, unpublished).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
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v1.4.0

23 Apr 03:12
@leightonpayne leightonpayne
v1.4.0
2988131
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v1.4.0

PADLOC-DB release v1.4.0

About

PADLOC-DB is a curated database of HMMs for prokaryotic antiviral defence system proteins, and models describing the genetic architecture of these systems. These files are used by PADLOC to locate antiviral defence systems in prokaryotic genomes. They can otherwise be used independently with HMMER 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 RM systems, new systems from Rousset et al. (https://doi.org/10.1016/j.chom.2022.02.018), darTG from LeRoux et al. (https://doi.org/10.1101/2021.09.27.462013), Gasdermins from Johnson et al. (https://doi.org/10.1126/science.abj8432), and spbK from Johnson et al. (https://doi.org/10.1371/journal.pgen.1010065).

What's included

padloc-db
├── hmm/                        <- Defence protein HMMs.
├── sys/                        <- Defence system models.
├── hmm_meta.txt                <- Metadata for HMMs.
├── sys_meta.txt                <- Metadata for system models.
├── README.md                   <- Information regarding metadata fields.
├── RELEASE.md                  <- This file.
└── LICENSE                     <- Copyright information.

Release record

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

14 Feb 02:11
@leightonpayne leightonpayne
v1.3.0
dec52e3
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v1.3.0

PADLOC-DB release v1.3.0

About

PADLOC-DB is a curated database of HMMs for prokaryotic antiviral defence system proteins, and models describing the genetic architecture of these systems. These files are used by PADLOC to locate antiviral defence systems in prokaryotic genomes. They can otherwise be used independently with HMMER 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 BREX, DISARM, pArgonaute, Phosphorothioation systems (DND/PBE/SSP), Pycsar, Viperin, and several other types of defence systems (https://doi.org/10/g29b).

What's included

padloc-db
├── hmm/                        <- Defence protein HMMs.
├── sys/                        <- Defence system models.
├── hmm_meta.txt                <- Metadata for HMMs.
├── sys_meta.txt                <- Metadata for system models.
├── README.md                   <- Information regarding metadata fields.
├── RELEASE.md                  <- This file.
└── LICENSE                     <- Copyright information.

Release record

Release Date HMMs Classifications
v1.3.0 14/02/2022 2974 181
v1.2.0 11/11/2021 2360 126
v1.1.0 28/09/2021 2223 97
v1.0.0 05/08/2021 915 36
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v1.2.0

10 Nov 23:34
@leightonpayne leightonpayne
v1.2.0
bef66fe
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v1.2.0

PADLOC-DB release v1.2.0

About

PADLOC-DB is a curated database of HMMs for prokaryotic antiviral defence system proteins, and models describing the genetic architecture of these systems. These files are used by PADLOC to locate antiviral defence systems in prokaryotic genomes. They can otherwise be used independently with HMMER 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 is the third release of PADLOC-DB. It adds 'classic' abortive infection and bacteriophage exclusion systems, plus the recently discovered BstA system from Owen et al., 2021.

What's included

padloc-db
├── hmm/                        <- Defence protein HMMs.
├── sys/                        <- Defence system models.
├── hmm_meta.txt                <- Metadata for HMMs.
├── sys_meta.txt                <- Metadata for system models.
├── README.md                   <- Information regarding metadata fields.
├── RELEASE.md                  <- This file.
└── LICENSE                     <- Copyright information.

Release record

Release Date HMMs Classifications
v1.2.0 11/11/2021 2360 126
v1.1.0 28/09/2021 2223 97
v1.0.0 05/08/2021 915 36
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v1.1.0

28 Sep 03:11
@leightonpayne leightonpayne
v1.1.0
f7bf45e
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v1.1.0

PADLOC-DB release v1.1.0

About

PADLOC-DB is a curated database of HMMs for prokaryotic antiviral defence system proteins, and models describing the genetic architecture of these systems. These files are used by PADLOC to locate antiviral defence systems in prokaryotic genomes. They can otherwise be used independently with HMMER 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 is the second release of PADLOC-DB. It greatly expands upon the previous release through the addition of HMMs and system models for 27 CRISPR-Cas subtypes and 26 diverse types of defence systems from Gao et al., 2020. One HMM was deprecated (see hmm/deprecated/notes.txt).

What's included

padloc-db
├── hmm/                        <- Defence protein HMMs.
├── sys/                        <- Defence system models.
├── hmm_meta.txt                <- Metadata for HMMs.
├── sys_meta.txt                <- Metadata for system models.
├── README.md                   <- Information regarding metadata fields.
├── RELEASE.md                  <- This file.
└── LICENSE                     <- Copyright information.

Release record

Release Date HMMs Classifications
v1.1.0 28/09/2021 2223 97
v1.0.0 05/08/2021 915 36
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v1.0.0

06 Aug 02:56
@leightonpayne leightonpayne
v1.0.0
53f8fba
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v1.0.0

PADLOC-DB release v1.0.0

About

PADLOC-DB is a curated database of HMMs for prokaryotic antiviral defence system proteins, and models describing the genetic architecture of these systems. These files are used by PADLOC to locate antiviral defence systems in prokaryotic genomes. They can otherwise be used independently with HMMER 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 is the first release of PADLOC-DB. It contains HMMs and system models for CBASS and Doron/deity defence systems (i.e. Druantia, Gabija, Hachiman, Kiwa, Lamassu, Septu, Shedu, Thoeris, Wadjet and Zorya). It also contains HMMs and models for several new types of Doron defence systems we've discovered (manuscript in preparation).

What's included

padloc-db
├── hmm/                        <- Defence protein HMMs.
├── sys/                        <- Defence system models.
├── hmm_meta.txt                <- Metadata for HMMs.
├── sys_meta.txt                <- Metadata for system models.
├── README.md                   <- Information regarding metadata fields.
├── RELEASE.md                  <- This file.
└── LICENSE                     <- Copyright information.

Release record

Release Date HMMs Classifications
1.0.0 05/08/2021 915 36
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