Abstract
Background: Genomic and genetic studies often require a target list of genes
before conducting any hypothesis testing or experimental verication. With the
ever-growing number of sequenced genomes and a variety of dierent annotation strategies, comes the potential for ambiguous gene symbols, making it cumbersome to capture the "correct" set of genes. In this article, we present and describe the Avian Immunome DB (Avimm) for easy gene property extraction as exemplied by avian immune genes. The avian immune system is characterised by a cascade of complex biological processes underlaid by more than 1000 dierent genes. It is a vital trait to study particularly in birds considering that they are a signicant driver in spreading zoonotic diseases. With the completion of phase II of the B10K ("Bird 10,000 Genomes") consortium's whole-genome sequencing eort, we have included 363 annotated bird genomes in addition to other publicly available bird genome data which serve as a valuable foundation for Avimm.
Construction and Content: A relational database with avian immune gene
evidence from Gene Ontology, Ensembl, UniProt and the B10K consortium has
been designed and set up. The foundation stone or the "seed" for the initial set
of avian immune genes is based on the well-studied model organism chicken
(Gallus gallus). Gene annotations, dierent transcript isoforms, nucleotide
sequences and protein information, including amino acid sequences, are included. Ambiguous gene names (symbols) are resolved within the database and linked to their canonical gene symbol. Avimm is supplemented by a command-line interface and a web front-end to query the database.
Utility and Discussion: The internal mapping of unique gene symbol identiers
to canonical gene symbols allows for an ambiguous gene property search. The
database is organised within core and feature tables, which makes it
straightforward to extend for future purposes. The database design is ready to be applied to other taxa or biological processes. Currently, the database contains 1170 distinct avian immune genes with canonical gene symbols and 645 synonyms across 363 bird species. While the command-line interface readily integrates into bioinformatics pipelines, the intuitive web front-end with
download functionality oers sophisticated search functionalities and tracks the
origin for each record. Avimm is publicly accessible at https://avimm.ab.mpg.de.
before conducting any hypothesis testing or experimental verication. With the
ever-growing number of sequenced genomes and a variety of dierent annotation strategies, comes the potential for ambiguous gene symbols, making it cumbersome to capture the "correct" set of genes. In this article, we present and describe the Avian Immunome DB (Avimm) for easy gene property extraction as exemplied by avian immune genes. The avian immune system is characterised by a cascade of complex biological processes underlaid by more than 1000 dierent genes. It is a vital trait to study particularly in birds considering that they are a signicant driver in spreading zoonotic diseases. With the completion of phase II of the B10K ("Bird 10,000 Genomes") consortium's whole-genome sequencing eort, we have included 363 annotated bird genomes in addition to other publicly available bird genome data which serve as a valuable foundation for Avimm.
Construction and Content: A relational database with avian immune gene
evidence from Gene Ontology, Ensembl, UniProt and the B10K consortium has
been designed and set up. The foundation stone or the "seed" for the initial set
of avian immune genes is based on the well-studied model organism chicken
(Gallus gallus). Gene annotations, dierent transcript isoforms, nucleotide
sequences and protein information, including amino acid sequences, are included. Ambiguous gene names (symbols) are resolved within the database and linked to their canonical gene symbol. Avimm is supplemented by a command-line interface and a web front-end to query the database.
Utility and Discussion: The internal mapping of unique gene symbol identiers
to canonical gene symbols allows for an ambiguous gene property search. The
database is organised within core and feature tables, which makes it
straightforward to extend for future purposes. The database design is ready to be applied to other taxa or biological processes. Currently, the database contains 1170 distinct avian immune genes with canonical gene symbols and 645 synonyms across 363 bird species. While the command-line interface readily integrates into bioinformatics pipelines, the intuitive web front-end with
download functionality oers sophisticated search functionalities and tracks the
origin for each record. Avimm is publicly accessible at https://avimm.ab.mpg.de.
| Original language | English |
|---|---|
| Journal | BMC Bioinformatics |
| Early online date | 12 Nov 2020 |
| DOIs | |
| Publication status | E-pub ahead of print - 12 Nov 2020 |
Keywords / Materials (for Non-textual outputs)
- B10K
- avian
- immunogenomics
- immunology
- immunome
- trait database