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OMAmer

OMAmer is a novel alignment-free protein family assignment method, which limits over-specific subfamily assignments and is suited to phylogenomic databases with thousands of genomes. It is based on an innovative method using evolutionnary-informed k-mers for alignment-free mapping to ancestral protein subfamilies. Whilst able to reject non-homologous family-level assignments, it has provided better and quicker subfamily-level assignments than a method based on closest sequences (using DIAMOND).

Installation

Requires Python >= 3.6. Download the package from the PyPI, resolving the dependencies by using pip install omamer.

Alternatively, clone this repository and install manually.

Pre-Built Databases

Download pre-built databases from the link below (from January 2020 OMA release).

DOI

  • LUCA.h5
  • Metazoa.h5
  • Viridiplantae.h5
  • Hominidae.h5

Their names indicate the root-taxon parameter used. Other non-required parameters were left to default.

omamer mkdb - Building a Database

This is currently reliant on the OMA browser's database file and the species phylogeny of HOGs. Building using OrthoXML files available shortly.

Usage

Required arguments: --db, --oma_path

usage: omamer mkdb [-h] --db DB [--nthreads NTHREADS] [--min_fam_size MIN_FAM_SIZE] [--min_fam_completeness MIN_FAM_COMPLETENESS] [--logic {AND,OR}]
                   [--root_taxon ROOT_TAXON] [--hidden_taxa HIDDEN_TAXA] [--species SPECIES] [--reduced_alphabet] [--k K] --oma_path OMA_PATH
                   [--log_level {debug,info,warning}]

Arguments

Flag Default Description
--db Path to new database (including filename)
--nthreads 1 Number of threads to use
--min_fam_size 6 Only root-HOGs with a protein count passing this threshold are used.
--min_fam_completeness 0.0 Only root-HOGs passing this threshold are used. The completeness of a HOG is defined as the number of observed species divided by the expected number of species at the HOG taxonomic level.
--logic AND Logic used between the two above arguments to filter root-HOGs. Options are "AND" or "OR".
--root_taxon LUCA HOGs defined at, or descending from, this taxon are uses as root-HOGs.
--hidden_taxa The proteins from these taxa are removed before the database computation. Usage: a list of comma-separated taxa (scientific name) with underscore replacing spaces (e.g. Bacteria,Homo_sapiens).
--species Temporary option
--reduced_alphabet Use reduced alphabet from Linclust paper
--k 6 k-mer length
--oma_path Path to a directory with both OmaServer.h5 and speciestree.nwk
--log_level info Logging level

omamer search - Searching a Database

Assign proteins to families and subfamilies in a pre-existing database.

Usage

Required arguments: --db, --query

usage: omamer search [-h] --db DB --query QUERY [--score {default,sensitive}] [--threshold THRESHOLD] [--reference_taxon REFERENCE_TAXON] [--out OUT]
                     [--include_extant_genes] [--chunksize CHUNKSIZE] [--nthreads NTHREADS] [--log_level {debug,info,warning}]

Arguments

Quick reference table

Flag Default Description
--db Path to existing database (including filename)
--query Path to FASTA formatted sequences
--score default Type of OMAmer-score to use. Options are "default" and "sensitive".
--threshold 0.05 Threshold applied on the OMAmer-score that is used to vary the specificity of predicted HOGs. The lower the theshold the more (over-)specific predicted HOGs will be.
--reference_taxon The placement is stopped when reaching a HOG with the reference taxon (must exist in the OMA database). This is a complementary option to vary the specificity of predicted HOGs.
--out stdout Path to output (default stdout)
--include_extant_genes Include extant gene IDs as comma separated entry in results
--chunksize 10000 Number of queries to process at once.
--nthreads 1 Number of threads to use
--log_level info Logging level

Output columns

Query sequence identifier

The sequence identifier from the input fasta

Predicted HOG identifier

The identifier of the hierarchical orthologous group (HOG) in OMA, which you can access through the OMA browser search bar or its REST API (https://omabrowser.org/api/docs).

A HOG identifier is composed of the root-HOG identifier (following “HOG:” and before the first dot), which is followed by its sub-HOGs (before each subsequent dot). For example, for subfamily HOG:0487954.3l.27l, HOG:0487954 is the root-HOG (HOG without-parent), HOG:0487954.3l is its child and HOG:0487954.3l.27l its grandchild.

Closest taxon from reference taxon

The taxon from the predicted HOG that is closest from the reference taxon (given one was provided). This option provides a mean to evaluate the performance of OMAmer placement given some knowledge of the query taxonomy is available.

Overlap-score

The fraction of the query sequence overlapping with k-mers of reference root-HOGs. This score aims to help reject partial homologous matches that are problematic in some applications.

Family-level OMAmer-score

The OMAmer-score of the predicted root-HOG. At the family level, this score measures the sequence similarity between the query and a given root-HOG.

Subfamily-level OMAmer-score

The OMAmer-score of the predicted HOG. At the subfamily level, this score captures the excess of similarity that is shared between the query and a given HOG, thus excluding the similarity with regions conserved in more ancestral HOGs.

Subfamily gene set

Extant gene IDs of predicted HOG, which you can look for in the OMA browser search bar or its REST API (https://omabrowser.org/api/docs).

Change log

Version 0.2.2

  • Automated deployment to PyPI
  • Removed PyHAM dependency

Version 0.2.0

  • Added --min_fam_completeness, --logic, --score and --reference_taxon options
  • New output format
  • Debugging

Version 0.1.2 - 0.1.3

  • Debugging

Version 0.1.0

  • Added hidden_taxa and threshold arguments

Version 0.0.1

  • Initial release

License

OMAmer is a free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

OMAmer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.

You should have received a copy of the GNU Lesser General Public License along with OMAmer. If not, see http://www.gnu.org/licenses/.

Citation

Victor Rossier, Alex Warwick Vesztrocy, Marc Robinson-Rechavi, Christophe Dessimoz, OMAmer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches, Bioinformatics, 2021;, btab219, https://doi.org/10.1093/bioinformatics/btab219

Code used for that paper is available here: DOI

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OMAmer - tree-driven and alignment-free protein assignment to sub-families

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