How does the search work?

Input a query in the search field. Everytime you press Space or Enter after a word, a token will be created. The token is composed of a prefix describing how the query should be treated and the actual query itself.

What are the different types of tokens?

Each token represents either a Gene, HOG, OMA group, or Taxon. Prefixes are used to specify which category to associate with the query term.

Category	Prefixes
Genes	id, go, ec, description, domain, sequence
HOGs	hog, sequence
OMA Groups	omagroup, fingerprint, sequence
Taxon	species, taxid, taxon

For example, the token [go:4225] will search for genes in the OMA database annotated with the GO:0004225 gene ontology term.
How to search for a multi-word query?

If your query term is composed of multiple words (e.g homo sapiens), use " " to encapsulate it.

How many tokens can I have?

There is no limit on the number of tokens. It is not possible to enter multiple tokens of different categories, except taxon, which can be combined with other categories. For example, you can search for 'hog:60627 species:HUMAN' to return human genes found in HOG:606207.

How to edit/delete a token?

To edit a query, click on it to modify the input field. To edit a prefix, click on the dropdown icon to select another one. To remove a token, click on the x to delete it.

Autosuggest

Typing a query without hitting enter or space will prompt an autosuggestion for the identifier after a few seconds.

Search

How does the search work?

Input a query in the search field. Everytime you press Space or Enter after a word, a token will be created. The token is composed of a prefix describing how the query should be treated and the actual query itself.

What are the different types of tokens?

Each token represents either a Gene, HOG, OMA group, or Taxon. Prefixes are used to specify which category to associate with the query term.

Category	Prefixes
Genes	id, go, ec, description, domain, sequence
HOGs	hog, sequence
OMA Groups	omagroup, fingerprint, sequence
Taxon	species, taxid, taxon

For example, the token [go:4225] will search for genes in the OMA database annotated with the GO:0004225 gene ontology term.
How to search for a multi-word query?

If your query term is composed of multiple words (e.g homo sapiens), use " " to encapsulate it.

How many tokens can I have?

There is no limit on the number of tokens. It is not possible to enter multiple tokens of different categories, except taxon, which can be combined with other categories. For example, you can search for 'hog:60627 species:HUMAN' to return human genes found in HOG:606207.

How to edit/delete a token?

To edit a query, click on it to modify the input field. To edit a prefix, click on the dropdown icon to select another one. To remove a token, click on the x to delete it.

Autosuggest

Typing a query without hitting enter or space will prompt an autosuggestion for the identifier after a few seconds.

OMA Academy

Welcome to the OMA Academy! Here, you will find interactive exercises designed to help you become familiar with orthology, phylogenies, and comparative genomics.

Background

OMA (“Orthologous MAtrix”) is a method and database for inferring orthologs across complete genomes, available at omabrowser.org. Many of the exercises use the OMA Browser as a starting point, while the OMA pipeline can also be run on custom genomic data using the FastOMA software.

Table of contents

Learning objectives

Navigate the OMA Browser to extract different types of homology information and trace evolutionary events such as duplications, gains, and losses.

Rapidly place new sequences into precomputed Hierarchical Orthologous Groups (HOGs).

Assess the quality of protein-coding gene annotations.

Install and run FastOMA to infer orthology on your own genomes.

Build and evaluate species trees.

Generate consensus annotations using evolutionary data.

Useful materials

When undertaking these exercises, the following materials may be useful:

OMA Help pages: Orthology Basics, Types of homologs, Access the OMA Data, Catalog of Tools, and Glossary

FastOMA documentation

OMA Primer

F1000 phylogenetics tree paper

OMA Standalone blog post

For Modules 2-5, it is best to use the GitPod workspace available here.

You will find the following buttons to interact with the exercises:

Asking questions

We remain available to answer your questions after this course. Please direct your emails to [email protected] with a subject starting with "OMA Academy".

However, for some general questions about OMA, we often receive requests through BioStars. Please consider asking your question there, including the tags "OMA" and "orthologs". We monitor BioStars for such questions and will answer them directly on that platform.