PADLOC-DB

About

This repo contains the latest version of the HMMs and system models used by PADLOC. The latest version of this database can be downloaded by running padloc --db-update.

The following document describes each field of hmm_meta.txt and sys_meta.txt, and how you can use your own HMMs and system models with PADLOC.

Citation

Manuscript in preparation.

System models

System models are written using YAML syntax:

---
maximum_separation: 4       <- Number of unrelated genes allowed to separate each component.
minimum_core: 4             <- Number of core genes that need to be present.
minimum_total: 5            <- Number of total genes that need to be present.
core_genes:                 <- Genes that are generally considered essential.
  - GenA
  - GenB
  - GenC
  - GenD
optional_genes:             <- Genes that are not always present.
  - GenX
  - GenY
prohibited_genes:           <- Genes that cannot be present.
  - GenZ
...

HMM metadata (hmm_meta.txt)

Compulsory fields

These fields must be filled out for use with PADLOC.

Field	Example	Description
hmm.accession	PDLC00001	A unique identifier for each padlocDB HMM.
hmm.name	GajA_6	Another unique identifier for each HMM. If the HMM is from an external database, the original ID from that database is preferred.
hmm.description	Predicted ATPase	A one line description of the HMM e.g. describing protein function or domains.
protein.name	PemK|MazF	The name of the protein that the HMM represents. Multiple protein names are separated by '|'. Capitalisation of the first letter is preferred. These are the names that are referenced in the system models.
e.value.threshold	1e-05	The minimum E-value allowed when reporting hits.
hmm.coverage.threshold	0.3	The proportion of the HMM that must contribute to the HMM/target alignment when reporting hits.
target.coverage.threshold	0.3	The proportion of the target that must contribute to the HMM/target alignment when reporting hits.
comment	NA	Other information that is relevant. This may include comments from the original database where applicable.

Optional fields

These fields are for reference only, and are not strictly required by PADLOC.

Field	Example	Description
secondary.name	CRISPR-accessory	A secondary identifier that can be referred to in the system definition for groups of proteins rather than individual protein names
system	DISARM, RESTRICTION MODIFICATION	The category of defence system to which the HMM belongs. Multiple system names are separated by ', '. The full system name is used where reasonable.
author	Payne LJ, Jackson SA	Author(s) of the entry. If the HMM is from an external database, crediting the original author is preferred. If the HMM is from a study where an author was not explicity credited, authorship is attributed to the first author of the study. Multiple authors are separated by ', '.
hmm.nseq	49	The number of sequences that contribute to the HMM.
hmm.length	120	The length of the the HMM.
literature.ref	10/f2wkj3	The DOI for the literature that implies that the members of the HMM belong to the protein/defence system. Multiple references are separated by ', '.
database.ref	PFAM; PF06527	Reference to the original accession of the alignment/HMM if it was taken from an external database, e.g. PFAM, COG, etc. Includes the name of the database name and the identifier separated by '; '.

System metadata (sys_meta.txt)

Compulsory fields

Field	Example	Description
yaml.name	druantia_type_I	The exact name of the yaml file that corresponds with the system type (without the .yaml extension)
search	T	Set to TRUE or FALSE (or T / F) to determine whether the system is searched or not.
comment	NA	Other information that is relevant.

Optional fields

Field	Example	Description
system.name	Druantia	The name of the system
type	type I	The subtype of the system.

Adding to the database

Additional HMMs and system models can be added directly to your copy of this database, or a separate database can be set up in the same way as this one.

Additional HMMs can be added to the hmm/ directory, hmm_meta.txt also needs to be updated to include metadata for the new HMMs. When using with PADLOC, these HMMs need to be concatenated into a single file in the hmm/ directory called padlocdb.hmm.

Additional system models can be added to the sys/ directory, sys_meta.txt should also be updated to include metadata for the new models.